Comprehensive Genomic Analysis Identifies a Diverse Landscape of Sideroblastic and Nonsideroblastic Iron-Related Anemias with Novel and Pathogenic Variants in an Iron-Deficient Endemic Setting

Inherited iron metabolism defects are possibly missed or underdiagnosed in iron-deficient endemic settings because of a lack of awareness or a methodical screening approach. Hence, we systematically evaluated anemia cases (2019 to 2021) based on clinical phenotype, normal screening tests (high-performance liquid chromatography, α gene sequencing, erythrocyte sedimentation rate, C-reactive protein, and tissue transglutaminase), and abnormal iron profile by targeted next-generation sequencing (26-gene panel) supplemented with whole-exome sequencing, multiplex ligation probe amplification/mitochondrial DNA sequencing, and chromosomal microarray. Novel variants in ALAS2, STEAP3, and HSPA9 genes were functionally validated. A total of 290 anemia cases were screened, and 41 (14%) enrolled for genomic testing as per inclusion criteria. Comprehensive genomic testing revealed pathogenic variants in 23 of 41 cases (56%). Congenital sideroblastic anemia was the most common diagnosis (14/23; 61%), with pathogenic variations in ALAS2 (n = 6), SLC25A38 (n = 3), HSPA9 (n = 2) and HSCB, SLC19A2, and mitochondrial DNA deletion (n = 1 each). Nonsideroblastic iron defects included STEAP3-related microcytic anemia (2/23; 8.7%) and hypotransferrenemia (1/23; 4.3%). A total of 6 of 22 cases (27%) revealed a non-iron metabolism gene defect on whole-exome sequencing. Eleven novel variants (including variants of uncertain significance) were noted in 13 cases. Genotype-phenotype correlation revealed a significant association of frameshift/nonsense/splice variants with lower presentation age (0.8 months versus 9 years; P < 0.01) compared with missense variants. The systematic evaluation helped uncover an inherited iron defect in 41% (17/41) of cases, suggesting the need for active screening and awareness for these rare diseases in an iron-deficient endemic population.

Integrated analysis of transcriptome and genome variations in pediatric T cell acute lymphoblastic leukemia: data from north Indian tertiary care center

INTRODUCTION

T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease with poor prognosis and inferior outcome. Although multiple studies have been perform on genomics of T-ALL, data from Indian sub-continent is scarce.

METHODS

In the current study we aimed to identify the genetic variability of T-ALL in an Indian cohort of pediatric (age ≤ 12 years) T-ALL patients (n = 25) by whole transcriptome sequencing along with whole exome sequencing and correlated the findings with clinical characteristics and disease outcome.

RESULTS

The median age was 7 years (range 3 -12 years). RNA sequencing revealed a definitive fusion event in 14 cases (56%) (including a novel fusions) with STIL::TAL1 in 4 (16%), followed by NUP21::ABL1, TCF7::SPI1, ETV6::HDAC8, LMO1::RIC3, DIAPH1::JAK2, SETD2::CCDC12 and RCBTB2::LPAR6 in 1 (4%) case each. Significant aberrant expression was noted in RAG1 (64%), RAG2 (80%), MYCN (52%), NKX3-1 (52%), NKX3-2 (32%), TLX3 (28%), LMO1 (20%) and MYB (16%) genes. WES data showed frequent mutations in NOTCH1 (35%) followed by WT1 (23%), FBXW7 (12%), KRAS (12%), PHF6 (12%) and JAK3 (12%). Nearly 88.2% of cases showed a deletion of CDKN2A/CDKN2B/MTAP genes. Clinically significant association of a better EFS and OS (p=0.01) was noted with RAG2 over-expression at a median follow up of 22 months, while a poor EFS (p=0.041) and high relapse rate (p=0.045) was observed with MYB over-expression.

CONCLUSION

Overall, the present study demonstrates the frequencies of transcriptomic and genetic alterations from Indian cohort of pediatric T-ALL and is a salient addition to current genomics data sets available in T-ALL.

Genomics of iron refractory iron deficiency anemia phenotype reveals a spectrum of novel pathogenic biallelic and monoallelic TMPRSS6 variants and rare overlapping disorders

The study highlights genomic findings in a series of 13 IRIDA phenotype cases. All had microcytic hypochromic anemia with suboptimal oral iron response to two different oral iron preparations at 4-6 weeks and low-normal ferritin, low transferrin saturation, and inappropriately high hepcidin. Targeted NGS on a 26-gene iron panel revealed pathogenic TMPRSS6 variants in 5/13 (38 %) cases. In addition, 2 (15 %) cases revealed rare SMAD4 and TBXAS1 gene variants that can present with refractory anemia but were consistent with diagnosis of hereditary hemorrhagic telangiectasia and Ghosal hematodiaphyseal dysplasia respectively.

Novel lncRNAs LINC01221, RP11-472G21.2 and CRNDE are markers of differential expression in pediatric patients with T cell acute lymphoblastic leukemia

INTRODUCTION

Pediatric T-cell acute lymphoblastic leukemia (T-ALL) poses significant challenges due to its aggressive nature and resistance to standard treatments. Long non-coding RNAs (lncRNAs) have emerged as potential biomarkers and therapeutic targets in leukemia. This study aims to characterize the lncRNA landscape in pediatric T-ALL, identify specific lncRNAs signatures, and assess their clinical relevance.

METHODS

RNA sequencing was performed on T-ALL patient and control samples. Differential expression analysis identified dysregulated lncRNAs and mRNAs. Functional enrichment analysis revealed potential roles of these lncRNAs in cancer pathogenesis. Validation of candidate lncRNAs was conducted using real-time PCR. Clinical correlations were assessed, including associations with patients' clinical characteristics and survival outcomes.

RESULTS

Analysis identified 674 dysregulated lncRNAs in pediatric T-ALL, with LINC01221 and CRNDE showing the most interactions in cancer progression pathways. Functional enrichment indicated involvement in apoptosis, survival, proliferation, and metastasis. Top 10 lncRNAs based on adjusted p value < 0.05 and Fold Change > 2 were selected for validation. Seven lncRNAs LINC01221, PCAT18, LINC00977, RP11-620J15.3, RP11-472G21.2, CTD-2291D10.4, and CRNDE showed correlation with RNA sequencing data. RP11-472G21.2 and CTD-2291D10.4 were highly expressed in T-ALL patients, with RP11-620J15.3 correlating significantly with better overall survival (p = 0.0007) at a median follow up of 32 months. The identified lncRNAs were further analysed in B-ALL patients. Distinct lncRNAs signatures were noted, distinguishing T-ALL from B-ALL and healthy controls, with lineage-specific overexpression of LINC01221 (p < 0.0001), RP11-472G21.2 (p < 0.001) and CRNDE (p = 0.04) in T-ALL.

CONCLUSION

This study provides insights into the lncRNA landscape of pediatric T-ALL, offering potential diagnostic and prognostic markers. RP11-620J15.3 emerges as a promising prognostic marker, and distinct lncRNAs signatures may aid in the differentiation of T-ALL subtypes. Further research with larger cohorts is warranted to validate these findings and advance personalized treatment strategies for pediatric T-ALL patients.

Additive effects of TPMT and NUDT15 on thiopurine toxicity in children with acute lymphoblastic leukemia across multiethnic populations

BACKGROUND

Thiopurines such as mercaptopurine (MP) are widely used to treat acute lymphoblastic leukemia (ALL). Thiopurine-S-methyltransferase (TPMT) and Nudix hydrolase 15 (NUDT15) inactivate thiopurines, and no-function variants are associated with drug-induced myelosuppression. Dose adjustment of MP is strongly recommended in patients with intermediate or complete loss of activity of TPMT and NUDT15. However, the extent of dosage reduction recommended for patients with intermediate activity in both enzymes is currently not clear.

METHODS

MP dosages during maintenance were collected from 1768 patients with ALL in Singapore, Guatemala, India, and North America. Patients were genotyped for TPMT and NUDT15, and actionable variants defined by Clinical Pharmacogenetics Implementation Consortium (CPIC) were used to classify patients as TPMT and NUDT15 normal metabolizers (TPMT/NUDT15 NM), TPMT or NUDT15 intermediate metabolizers (TPMT IM or NUDT15 IM), or TPMT and NUDT15 compound intermediate metabolizers (TPMT/NUDT15 IM/IM). In parallel, we evaluated MP toxicity, metabolism, and dose adjustment using a Tpmt/Nudt15 combined heterozygous mouse model (Tpmt  +/-/Nudt15  +/-).

RESULTS

Twenty-two patients (1.2%) were TPMT/NUDT15 IM/IM in the cohort, with the majority self-reported as Hispanics (68.2%, 15/22). TPMT/NUDT15 IM/IM patients tolerated a median daily MP dose of 25.7 mg/m2 (interquartile range [IQR], 19.0-31.1 mg/m2), significantly lower than TPMT IM and NUDT15 IM dosage (P< .001). Similarly, Tpmt  +/-/Nudt15  +/- mice displayed excessive hematopoietic toxicity and accumulated more metabolite (DNA-TG) than wildtype or single heterozygous mice, that was effectively mitigated by a genotype-guided dose titration of MP.

CONCLUSION

We recommend more substantial dose reductions to individualize MP therapy and mitigate toxicity in TPMT/NUDT15 IM/IM patients.

ITPA polymorphisms do not predict additional risk beyond TPMT and NUDT15 for thiopurine-induced cytopenia in inflammatory bowel disease

INTRODUCTION AND AIM

Thiopurine-related leukopenia is associated with polymorphisms in the thiopurine methyltransferase (TPMT) and nucleoside diphosphate-linked moiety X type motif 15 (NUDT15) genes. However, those polymorphisms explain only a fraction of thiopurine-related leukopenia. Our aim was to study the role of an inosine triphosphate pyrophosphatase (ITPA) polymorphism in patients with inflammatory bowel disease (IBD) and thiopurine-related leukopenia that was unexplained by the TPMT and NUDT15 polymorphisms.

MATERIAL AND METHODS

We enrolled consecutive IBD patients on thiopurines (azathioprine or 6-mercaptopurine) from January 2019-March 2020, at a tertiary care center in North India. The presence of the ITPA (C.94C > A) polymorphism was evaluated in all patients, along with its association with thiopurine-related leukopenia.

RESULTS

Of the 33 patients (from a total of 119 patients) that developed leukopenia, 8 had the TPMT (n = 1) or NUDT15 (n = 7) polymorphism. Of the remaining 111 patients, their mean age was 36.36 ± 13.54 years and 57 (51.3%) were males. Twenty-five (21.01%) had unexplained leukopenia. The ITPA polymorphism was detected in 4 (16%) patients in the unexplained leukopenia group and 24 (27.9%) patients in the non-leukopenia group (p = 0.228). The odds ratio for predicting leukopenia with the ITPA polymorphism was 0.4921 (95% CI 0.1520-1.5830, p = 0.234).

CONCLUSION

The ITPA (C.94C > A) polymorphism was frequently detected in the study population but was not predictive for leukopenia in patients with IBD on thiopurine therapy.

Iron Overload and Anemia in Rhesus Hemolytic Disease of Newborn: A Prospective Observational Study

This study assessed the prevalence of iron overload in infants born to Rh isoimmunized mothers. Infants born to Rh isoimmunized mothers with Indirect Coomb's Test (ICT) titers ≥1:16 were prospectively enrolled and followed until 3 mo. Hemoglobin and serum ferritin were estimated at birth and 3 mo of age. The outcomes were the incidence of iron overload (at birth and 3 mo), anemia, and the need for transfusions in the first 3 mo. Seventy-four infants were enrolled, nearly half receiving intrauterine transfusion (IUT). Sixty (82.2%) had hyperferritinemia at birth. The median (1st, 3rd quartile) ferritin levels were 456 (321, 631) μg/L. Infants who received IUTs had significantly higher serum ferritin levels at birth. Fifty-one (76.1%) infants had hyperferritinemia at 3 mo. Over three months of follow-up, 53 (71.6%) infants had anemia, of which 33 (48.5%) required packed red blood cells (PRBC) transfusion. These findings suggest that iron overload is common in these infants in the first 3 mo.

A Well-Curated Cost-Effective Next-Generation Sequencing Panel Identifies a Diverse Landscape of Pathogenic and Novel Germline Variants in a Bone Marrow Failure Cohort in a Resource-Constraint Setting

The current study is a 4-year experience in diagnosis and screening of inherited and immune bone marrow failure cases using a targeted sequencing panel. A total of 171 cases underwent targeted next-generation sequencing and were categorized as suspected inherited bone marrow failure syndrome (IBMFS) group (106; 62%) and immune/idiopathic aplastic anemia (IAA) group (65; 38%) based on clinical and laboratory criteria. A total of 110 (64%) were pediatric (aged 0 to 12 years) patients and 61 (36%) were adolescent and adult (aged 13 to 47 years) patients. In suspected IBMFS group, 47 (44%), and in IAA group, 8 (12%) revealed a likely germline pathogenic variation. Whole-exome sequencing performed in 15 of 59 suspected IBMFS group cases was negative on targeted panel, and revealed a clinically important variation in 3 (20%) cases. A total of 11 novel variants were identified. The targeted panel helped establish a diagnosis in 44% (27/61) of unclassified bone marrow failure syndrome cases and led to amendment of clinical diagnosis in 5 (4.7%) cases. Overall, diagnostic yield of this well-curated small panel was comparable to Western studies with larger gene panels. Moreover, this was achievable at a much lower cost, making it suitable for resource-constraint settings. In addition, high frequency (>10%) of cryptic pathogenic IBMFS gene variations in IAA cohort suggests routine incorporation of targeted next-generation sequencing screening in these cases.

A Randomized, Controlled, Noninferiority Trial Comparing Vitamin B12 Monotherapy Versus Combination Multinutrient Therapy with Vitamin B12 for Efficacy in Treatment of Infantile Tremor Syndrome

OBJECTIVES

To compare the mean Likert (caregiver impression of change) and CAPUTE scores in children with ITS treated with daily injectable vitamin B12 alone versus injectable vitamin B12 with other multinutrients at 1 wk and 1 mo of therapy.

METHODS

This was an open-label, active-controlled, assessor-blinded, noninferiority, randomized clinical trial. The participants included children aged 3 mo to 2 y with infantile tremor syndrome. Children were randomized to receive either 1 mg of daily injectable vitamin B12 or 1 mg of daily injectable vitamin B12 with other multinutrients (B12 + MV). Primary outcome measure was the mean Likert score in the two arms at 1 wk. Secondary outcome measures were mean change in CAPUTE scores at 1 wk of therapy; and mean change in CAPUTE and Vineland Social Maturity Scale (VSMS) scores after 1 mo of treatment.

RESULTS

Seventy-two (N = 72) of the 160 screened were enrolled and randomized. The mean (SD) Likert score in the B12 group (n = 38) was 16.1 (3.7) and in the B12 + MV group (n = 34) was 14.9 (3.7); p = 0.237. Mean (SD) change in CAPUTE (CAT/CLAMS) at 1 mo in the groups was not statistically different. The mean (SD) change in social quotient in the B12 monotherapy group, 35.0 (20.7) was significantly higher than the B12 + multinutrient group 23.5 (15.4); p=0.01.

CONCLUSION

Injectable vitamin B12 monotherapy in ITS resulted in an improvement that was noninferior to combination multinutrient therapy, strongly supporting vitamin B12 deficiency as the cause of infantile tremor syndrome.

TRIAL REGISTRATION

The trial was registered at CTRI.org (CTRI/2018/05/013841).

Evaluation of FTO polymorphism in 6-mercaptopurine related intolerance in children with acute lymphoblastic leukemia

PURPOSE

Thiopurine drugs like 6-Mercaptopurine (6MP) are the cornerstone of maintenance therapy in acute lymphoblastic leukemia (ALL). A recently described variant in alpha-ketoglutarate dependent dioxygenase (FTO) gene has been reported to play an important role in thiopurine induced myelosuppression.

METHODS

In this study, we genotyped a coding variant (p.Ala134Thr, rs79206939) and an intronic variant (rs16952570) of FTO in 174 Indian children (age ≤ 12 years) with ALL on maintenance phase of chemotherapy and examined correlation with the risk of thiopurine induced myelosuppression and hepatic toxicity.

RESULTS

The prevalence of FTO-rs16952570 polymorphism was 18.4% (32/174) with 142 (82%) cases having TT genotype, 26 (15%) cases with TC genotype and 6 (3.4%) cases having CC genotype. FTO-rs79206939 was absent and non-polymorphic in our study group. The mean dose of 6-MP during 36 weeks of maintenance of TT, TC and CC carriers of FTO-rs16952570 was 53.7, 53.6 and 54.1 mg/m2/day. Number of patients tolerating starting dose of 60 mg/m2/day was significantly higher in CC (50%) than TT/TC (14%) genotype carrying cases (p = 0.014). However, no statistical significance was observed for total leukocyte count (TLC), absolute neutrophil count (ANC) as well as for platelets counts in patients harboring FTO-rs16952570 TT/TC/CC genotype at 4, 8, 12, 24 and 36 weeks after start of thiopurine therapy. Further, no significant correlation was noted between number of weeks of chemotherapy interruptions or episodes of febrile neutropenia and no evidence of hepatotoxicity was found with the genotype studied.

CONCLUSION

Polymorphism in FTO-rs16952570 did not show any correlation with thiopurine related toxicity in ALL patients.

Novel device for automating exchange transfusions through umbilical venous route in neonates

Manually performed double-volume exchange transfusion (DVET) is tedious, error-prone, and may incur the risk of embolism. We aimed to develop a device that automates the DVET procedure performed through the umbilical venous route. We evaluated changes in blood passing through the device during DVET. We developed an electro-mechanical device with accessories (tubing and valve assembly) to perform a complete DVET. It comprises two syringes driven by a common pump that moves back and forth to withdraw aliquots of the patient's blood and infuse equal volumes of donor blood. In tandem, it draws donor blood from a blood bank bag and pushes the patient blood drawn from the previous cycle into a waste bag, respectively. One-way duckbill valves and a two-way pinch valve ensure the separation of the donor and patient blood. A sensor detects bubbles and clots. A dashboard displays set and measured parameters. We tested the accuracy of the delivered flow rate and volume, electrical safety, embolus detection, and changes in hematological and biochemical values. The delivered flow and volume were within 5% of the set parameters. All electrical safety parameters were within normal limits. The sensor consistently detected microbubbles and clots. There were no clinically significant differences in laboratory parameters between samples drawn directly from the blood bank bag and drawn from the exit port at 80, 100, 120, and 160 s with a fixed aliquot volume.

CONCLUSIONS

Our prototype of a novel device can safely automate a DVET. Further trials of this device are warranted.

WHAT IS KNOWN

• Double volume exchange transfusion is often performed manually, but this is time-consuming and error-prone. • Previous attempts at automation were not widely adopted because they involved inserting two catheters and did not have mechanisms to prevent embolism.

WHAT IS NEW

• This novel device fully automates double volume exchange transfusions through a single-lumen umbilical venous catheter. • It prevents air and clot embolism and has a screen for input and output parameters and alarms.

Increased fracture risk in Parkinson's disease - An exploration of mechanisms and consequences for fracture prediction with FRAX

The relative contributions of factors such as muscle strength, falls risk and low bone mineral density (BMD) to increased fracture risk in Parkinson's Disease (PD) were examined in an analysis of 5212 community-dwelling women age 75 years or more recruited to a randomised, double-blind, placebo-controlled study of the oral bisphosphonate, clodronate. Similar number of PD and non-PD subjects received treatment. Each participant had measurements of hip and forearm BMD, muscle strength (hand grip strength and maximum isometric quadriceps strength), ability in the sit-to-stand test, and postural stability. Incident radiographic and/or surgically verified fractures, and deaths, were recorded over an average follow-up of 3.8 years. A diagnosis of PD was made if it was self-reported and appropriate medication was recorded at the study entry. 47 of the women (0.9 %) had a diagnosis of PD at baseline. They were of similar age to those without PD, but reported higher disability scores and lower quality of life. While BMD at the forearm and hip regions was lower in PD, this only reached statistical significance at the femoral neck (0.61 ± 0.12 vs 0.65 ± 0.12 g/cm², p = 0.037). Right hand grip strength was non-significantly lower in PD, but maximum right quadriceps strength was much reduced (96.9 ± 49.3 vs 126.3 ± 59.2 N, p = 0.003). Eleven (23.4 %) of the women with PD sustained 12 fractures, while 609 women (11.8 %) without PD sustained 742 osteoporotic fractures. The risk of osteoporotic fracture associated with PD was 2.24-fold higher in women with PD (Cox-regression HR 2.24, 95 % CI 1.23-4.06) and this remained high when adjusted for death as a competing risk (2.17, 95 % CI 1.17-4.01, p = 0.013). Following adjustment for femoral neck BMD, PD remained a significant predictor of fracture (HR 2.04, 1.12-3.70, p = 0.020). Entering PD as a risk variable using the rheumatoid arthritis input as a surrogate resulted in a reduction in PD as a FRAX-independent risk factor, particularly when BMD was included in FRAX (1.65, 95 % CI), but the relationship between PD and fracture risk appears to remain of clinical significance. The study suggests that PD may be an independent input in future iterations of FRAX, possibly due to non-skeletal components of risk such as reduced lower limb muscle strength. Introducing measures of muscle strength and performance in FRAX could also be considered.

Early mortality continues to be a barrier to excellent survival in childhood acute promyelocytic leukemia: a retrospective study of 62 patients spanning 17 years

Data on childhood acute promyelocytic leukemia (APL) from low-and middle-income countries is limited. Early mortality is a concern and often not highlighted in clinical trials. The retrospective study was conducted on patients (≤12 years) with APL from 2003 to 2021 at a single center in India. Patients were treated with all-trans-retinoic acid (ATRA) and chemotherapy. Induction and three courses of consolidation were followed by maintenance for 2 years. In 2015, the protocol was updated with following modifications: (a) obtaining diagnostic cerebrospinal fluid at end-of-induction rather than at diagnosis, (b) administering intrathecal cytarabine regardless of risk-category, (c) risk-stratified administration of chemotherapy, and (d) inclusion of ATRA in all the cycles of consolidation. Sixty-two patients were diagnosed over the 17 years. The median age was 8 years (range: 0.9-12). Half had high-risk disease. Differentiation syndrome was observed in 32%, none being fatal. Eighteen (29%) patients died due to hemorrhage (83%) or septicemia (17%). Thirteen (21%) had early mortality (≤15 days), all due to hemorrhage. A platelet count <20 × 10⁹/L predicted early mortality (odds ratio: 4.5; 95% CI: 0.9-22, p = 0.06). Treatment abandonment reduced from 23.5% during 2003-2015 to nil during 2015-2021 (p = 0.006). Three (8%) patients relapsed. The 4-year OS of all patients and the patients who survived >15 days was 70.1% and 89.6%, respectively. The 4-year EFS, including abandonment and early mortality, before and following updated protocol, was 61.4% and 65.5%, respectively (p = 0.77). Early mortality continues to be a barrier to an otherwise excellent survival in childhood APL. A significant reduction in treatment abandonment in recent years is gratifying.

Therapy-Acquired Clonal Mutations in Thiopurine Drug-Response Genes Drive Majority of Early Relapses in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia

METHODS

Forty pediatric (0-12 years) B-ALL DNA samples (20 paired Diagnosis-Relapse) and an additional six B-ALL DNA samples (without relapse at 3 years post treatment), as the non-relapse arm, were retrieved from the biobank for advanced genomic analysis. Deep sequencing (1050-5000X; mean 1600X) was performed using a custom NGS panel of 74 genes incorporating unique molecular barcodes.

RESULTS

A total 47 major clones (>25% VAF) and 188 minor clones were noted in 40 cases after bioinformatic data filtering. Of the forty-seven major clones, eight (17%) were diagnosis-specific, seventeen (36%) were relapse-specific and 11 (23%) were shared. In the control arm, no pathogenic major clone was noted in any of the six samples. The most common clonal evolution pattern observed was therapy-acquired (TA), with 9/20 (45%), followed by M-M, with 5/20 (25%), m-M, with 4/20 (20%) and unclassified (UNC) 2/20 (10%). The TA clonal pattern was predominant in early relapses 7/12 (58%), with 71% (5/7) having major clonal mutations in the NT5C2 or PMS2 gene related to thiopurine-dose response. In addition, 60% (3/5) of these cases were preceded by an initial hit in the epigenetic regulator, KMT2D. Mutations in common relapse-enriched genes comprised 33% of the very early relapses, 50% of the early and 40% of the late relapses. Overall, 14/46 (30%) of the samples showed the hypermutation phenotype, of which the majority (50%) had a TA pattern of relapse.

CONCLUSIONS

Our study highlights the high frequency of early relapses driven by TA clones, demonstrating the need to identify their early rise during chemotherapy by digital PCR.

Evaluation of ultrasound airway assessment parameters in pregnant patients and their comparison with that of non-pregnant women: a prospective cohort study

BACKGROUND

Clinical airway assessment parameters differ significantly between pregnant and non-pregnant patients, however literature comparing their ultrasound (US) airway parameters is limited. We planned a prospective cohort study to compare US-assessed airway parameters between pregnant and non-pregnant women.

METHODS

We enrolled 82 pregnant females scheduled for elective cesarean section under neuraxial anesthesia and 80 age-matched non-pregnant females scheduled for elective surgery. Pre-operative clinical airway assessment was performed in both groups. The US airway assessment was done pre-operatively in non-pregnant and postoperatively in pregnant patients. Our primary objective was to compare US-assessed parameters, and secondary objectives included a comparison of clinical airway assessment parameters and investigating a relationship between a difficult airway (defined as a modified Mallampati grade (MMG) ≥ 3) and other airway assessment parameters.

RESULTS

Among several US airway parameters, pregnant patients had significantly higher hyomental distance, anterior neck soft tissue thickness at the hyoid and vocal cord level, and oral cavity height, while the tongue thickness and mandibular condylar movements were significantly lower than in non-pregnant patients. Similarly, for the clinical airway assessment, pregnant patients had significantly higher MMG and upper lip bite test scores, mentohyoid distance, and neck circumference. Pregnancy, the ratio of pre-epiglottic space and epiglottis-to-vocal cords distance (Pre-E/E-VC), and hyoid bone visibility were independent predictors of a difficult airway.

CONCLUSION

The US airway assessment parameters differ significantly between pregnant and non-pregnant patients. Pregnancy, hyoid bone visibility, and Pre-E/E-VC ratio were independent predictors of the difficult airway in female patients.

A randomized trial of once daily versus twice daily dosing of oral iron in CKD

We investigated the effect of two dosing regimens of oral iron on iron status and hematological parameters in patients with CKD. In this single center, open label, randomized, active controlled clinical trial, stable adult patients with CKD stage G3-4 with percentage transferrin saturation (%TSAT) ≤ 30% and serum ferritin ≤ 500 ng/ml were eligible. Participants were randomized to receive either 100 mg of ferrous ascorbate once daily (OD group) or 100 mg of ferrous ascorbate twice daily (BD group, total daily dose 200 mg). The primary outcome was change in %TSAT between groups over 12 weeks. The secondary outcomes were changes in other iron status and hematological parameters, serum interleukin-6 (IL-6) and hepcidin. 80 participants were enrolled out of which 76 completed the study. Change in %TSAT was not significantly different between groups (β = - 1.43, 95% CI - 3.99 to 1.12, BD group as reference). The rise in serum ferritin was less in the OD group as compared to BD group (β = - 0.36, 95% CI - 0.61 to - 0.10) whereas MCHC increased in the OD group as compared to decrease in the BD group (β = 0.37, 95% CI 0.067-0.67). These observations need exploration to ascertain the impact of different oral iron dosing strategies in CKD.

Exploring the genetic landscape of diphtheria, tetanus and pertussis vaccination-associated seizures or subsequent epilepsies

Background

Diphtheria, Tetanus, and whole-cell Pertussis (DTwP) vaccination-associated seizures form the commonest type of serious adverse event following immunization in India and are an important reason for vaccine hesitancy. Our study explored the genetic explanation of DTwP vaccination-associated seizures or subsequent epilepsies.

Methods

Between March 2017 and March 2019, we screened 67 children with DTwP vaccination-associated seizures or subsequent epilepsies, and of those, we studied 54 without prior seizures or neurodevelopmental deficits. Our study design was cross-sectional with a 1-year follow-up having both retrospective and prospective cases. We performed clinical exome sequencing focused on 157 epilepsy-associated genes and multiplex ligation-dependent probe amplification of the SCN1A gene at enrolment. We applied the Vineland Social Maturity Scale for neurodevelopmental assessment at follow-up.

Findings

Of 54 children enrolled and underwent genetic testing (median age 37.5 months, interquartile range 7.7-67.2; diagnosis at enrolment: epilepsy 29, febrile seizure 21, and febrile seizure-plus 4), we found 33 pathogenic variants of 12 genes. Of 33 variants, 13 (39%) were novel. Most pathogenic variants were found in SCN1A gene (n = 21/33; 64%), SCN8A in 2 children, and 10 children had one variant in CDKL5, DEPDC5, GNAO1, KCNA2, KCNT1, KCNQ2, NPRL3, PCDH19, RHOBTB2, and SLC2A1. Five or more seizures (odds ratio [OR] = 5.3, confidence interval [CI]: 1.6-18.4, p = 0.006), drug-resistant epilepsy (OR = 9.8, 95% CI: 2.6-30.7, p = 0.001) and neurodevelopmental impairment (social quotient < 70) (OR = 5.6, 95% CI: 1.65-17.6, p = 0.006) were significant predictors of genetic diagnosis.

Interpretation

Our study provides proof-of-concept for genetic aetiology in children with DTwP vaccination-associated seizures or subsequent epilepsies and has important implications for vaccination policies in developing countries.

Funding

International Pediatric Association Foundation, Inc. (IPAF): İhsan Doğramaci research award 2016/2017; Indian Council of Medical Research (ICMR), New Delhi, India: No.3/1/3/JRF-2016/HRD/LS/71/10940.

Clinico-hematological and Outcome Profile of Pediatric B-other-ALL and BCR::ABL1-like pre-B-ALL: An Integrated Genomic Study From North India

PURPOSE

BCR::ABL1-like pre-B-ALL comprises a myriad of genetic lesions making molecular diagnosis challenging and expensive. Its frequency and outcome are less studied in resource-constraint settings.

METHODS

154 pre-B-ALL cases (0-12 years) were enrolled as group 1 (37 cases of B-other-ALL) and group 2 (117 patients with recurrent translocations/ hyperdiploidy). Group 1 was evaluated for BCR::ABL1-like genetic lesions and copy-number abnormalities (CNAs) as per our published PACE approach supplemented with targeted RNA sequencing.

RESULTS

BCR::ABL1-like frequency was 5.2% (8 of 154) and 22% (8 of 37) with the PACE approach alone in the whole and B-other-ALL cohort, respectively. The addition of targeted RNA-sequencing had led to the frequency increasing to 9% (14 of 154) and 38% (14 of 37) in the whole and B-other-ALL cohort, respectively. P2RY8::CRLF2, IGH::CRLF2, and RCSD1::ABL1 were noted in 8 (57.1%), 4 (28.6%), and 2 (14.3%) patients, respectively. CNAs were noted in 56.7% (21 of 37) of patients. The BCR::ABL1-like group had a significantly higher initial WBC count of ≥ 50,000/mm³ (71.4%; P < .001) than group 2. The 4-year OS, EFS, RFS of group 1 was not statistically different from group 2, though RFS was borderline poor (84.2%, 51.7%, 56.9% Vs. 82.6%, 62.9%, 78% [P - .42, P - .53, P - .059]). The 4-year EFS and RFS for BCR::ABL1-like cases was 70.7% and 76.6%, respectively.

CONCLUSIONS

The sensitivity of detecting BCR::ABL1-like lesions had increased significantly from 22% using the PACE approach alone to 38% in B-other-ALLs with the integrated approach. Although outcomes were not statistically different, a higher percentage of relapses were noted in the B-other-ALL group.

Estimation of iron overload with T2*MRI in children treated for hematological malignancies

Iron overload may contribute to long-term complications in childhood cancer survivors. There are limited reports of assessment of tissue iron overload in childhood leukemia by magnetic resonance imaging (MRI). A cross-sectional, observational study in children treated for hematological malignancy was undertaken. Patients ≥6 months from the end of therapy who had received ≥5 red-cell transfusions were included. Iron overload was estimated by serum ferritin (SF) and T2*MRI. Forty-five survivors were enrolled among 431 treated for hematological malignancies. The median age at diagnosis was 7-years. A median of 8 red-cell units was transfused. The median duration from the end of treatment was 15 months. An elevated SF (>1,000 ng/ml), elevated liver iron concentration (LIC) and myocardial iron concentration (MIC) were observed in 5 (11.1%), 20 (45.4%), and 2 (4.5%) patients, respectively. All survivors with SF >1,000 ng/ml had elevated LIC. The LIC correlated with SF (p < 0.001). MIC lacked correlation with SF or LIC. Factors including the number of red-cell units transfused and duration from the last transfusion were associated with elevated SF (p = 0.001, 0.002) and elevated LIC (p = 0.012, 0.005) in multiple linear regression. SF >595 ng/ml predicted elevated LIC with a sensitivity of 85% and specificity of 91.6% (AUC 91.2%). A cutoff >9 units of red cell transfusions had poor sensitivity and specificity of 70% and 75% (AUC 76.6%) to predict abnormal LIC. SF >600 ng/ml is a robust tool to predict iron overload, and T2*MRI should be considered in childhood cancer survivors with SF exceeding 600 ng/ml.

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

BACKGROUND

Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications.

METHODS

We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC).

FINDINGS

In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683-0·717]).

INTERPRETATION

In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required.

FUNDING

British Journal of Surgery Society.

Aetiological Profile and Short-Term Neurological Outcome of Haemorrhagic Stroke in Children

BACKGROUND

Haemorrhagic stroke (HS) accounts for nearly half of the paediatric strokes. The aetiology of HS in childhood is not well defined in the Indian context.

OBJECTIVES

To study the aetiological profile and short-term neurological outcome of children with HS from North India.

METHODS

In a prospective observational study, consecutive patients >28 days to <12 years of age admitted with a diagnosis of HS were enrolled. Demography, clinical, radiological details and investigations were recorded. Short-term outcomes were assessed at three months follow-up with the Paediatric Cerebral Performance Category scale and Paediatric Stroke Outcome Measure (PSOM).

RESULTS

A total of 48 children with HS were enrolled. The median age was 6 months (1-58 months), and 33 (69%) were <2 years old. Vitamin K deficiency-related bleeding disorder (VKDB, 44%), central nervous system infections (19%), arteriovenous malformations (13%) and inherited coagulation disorders (8%) were the most common risk factors for HS. VKDB and inherited coagulation disorders were more frequent in children <2 years of age, and arteriovenous malformations were more frequent in children >2 years of age (p = 0.001). During hospitalization, 21 (44%) children died. Older age, low Glasgow coma score (<8) at admission and paediatric intracerebral haemorrhage score ≥2 were associated with mortality at discharge (p = <0.05). Among survivors, 15 (56%) children had neurological deficits (PSOM >0.5) at three month follow-up.

CONCLUSION

VKDB, inherited coagulation disorders, central nervous system infections and arteriovenous malformations were the most common risk factors for HS. VKDB is the single most important preventable risk factor for HS in infants.

'FLT3-ITD Mutation Does Not Influence Survival Outcome in Adult Acute Promyelocytic Leukemia Patients Treated With ATO and ATRA-Based Therapeutic Regimen: Experience From a North Indian Tertiary Care Centre'

INTRODUCTION

NPM1 and FLT3-ITD are frequently mutated genes in acute myeloid leukemia. We studied clinico-hematological profile and survival outcome of adult acute promyelocytic leukemia (APL) patients harboring these mutations.

MATERIALS AND METHODS

De novo APL cases (> 12 years), enrolled between January 2019 and June 2020, were evaluated for FLT3-ITD and NPM1 mutations (A, B, D mutations) by conventional and real-time qualitative PCR respectively.

RESULTS

FLT3-ITD mutation was detected in 12 of 36 (33.3%) de novo APLs cases while NPM1 mutation was not detected. FLT3-ITD was more frequently associated with Sanz high-risk category as compared to the intermediate-risk category (75% vs. 29%, P = .02), with BCR3 transcript type (P = .08) and higher median WBC count [22.7 × 10⁹/L)(range 1.3-184), P = .018]. One and half-years overall survival (OS) and event-free survival (EFS) were not significantly altered by the presence/absence of FLT3-ITD mutation (OS 86% vs. 70%, P = .32; EFS 86% vs. 70%, P = .33), between genders (OS, EFS both 89% in males vs. 69% in females, P = .15) and between adolescent and younger adults (AYA) (≤ 30 years) and older adult APL cases (> 30 years) (OS 86% vs. 78%, P = .55; EFS 85% vs. 77%, P = .55), however were significantly lower with BCR3 transcript as compared to BCR1 transcript (OS 56% vs. 91%, P = .019; EFS 56% vs. 91%, P = .016) in univariate analysis, although not in multivariate analysis. One and half-year OS and EFS was 57% (6/14, P = .009 for each) in high-risk APL.

CONCLUSION

FLT3-ITD mutation did not influence survival outcome in adult APL treated with ATO and ATRA-based therapeutic regimen.

Clinical and Genetic Spectrum of Inborn Errors of Immunity in a Tertiary Care Center in Southern India

OBJECTIVES

To study the incidence, clinical manifestations, and genetic spectrum of primary immunodeficiency diseases (PID)/inborn errors of immunity (IEI) in a tertiary care hospital in Southern India.

METHODS

A retrospective analysis of all patients with a clinical suspicion of PID/IEI seen at a tertiary care hospital was performed. All patients had at least one or more warning signs of PID. Serum immunoglobulin levels and other targeted investigations were performed as warranted by the clinical presentation. All families with suspected PID were counseled and offered genetic testing.

RESULTS

A total of 225 children were evaluated for PID during the study period of 6 y. Fifty-six of them did not meet the European Society of Immunodeficiencies (ESID) criteria (working definition of clinical diagnosis) and were excluded. An IEI was found in 30/49 (61.2%) patients. The most frequent reason for referral was recurrent/unusual or serious infections (28%), or cytopenia (16%). Group IV diseases of immune dysregulation was the most common category (19%), followed by group III predominant antibody deficiencies in 23/163 (14%), as per the International Union of Immunological Societies (IUIS) classification.

CONCLUSIONS

This study highlights the heterogeneity of the present cohort, the underuse of genetic tests, and efforts to provide optimal care for children with possible IEI in this center.

Experience of quantity and quality of DNA and RNA extraction from limited pediatric blood samples: A comparative analysis of automated and manual kit-based method

INTRODUCTION

Optimal DNA and RNA quantity and purity is essential for downstream molecular biology experimentation and to avoid re-processing of sample. Despite availability of different kits and automated systems for nucleic acid isolation there is limited data on their performance evaluation, more so with pediatric blood samples, that are usually compromised in quantity. Hence, we evaluated the performance of automated QIAcube platform using pediatric blood samples in parallel with manual Qiagen extraction kits.

MATERIALS AND METHODS

: A total of 500 samples were analyzed based on groups of PBMC and direct blood input. The isolated DNA and RNA were surveyed for quantity and quality tests by spectrophotometric and downstream analysis.

RESULTS

: There was no significant difference in the DNA quantity (ng/ul) between manual and automated method based on similar sample input but quality (260/280) was significantly better with the QIAcube platform when direct blood and or PBMCs were used for extraction respectively (1.82 ± 004 Vs. 1.84.002; P-0.000008 and 1.859 ± 005 Vs. 1.843 ± 0.003; P-0.02). Moreover, the standard error mean was low for both quantity and quality in the QIAcube method suggesting uniformity. Comparison of quality assessment by spectrophotometer and qubit fluorimeter showed that QIAcube sheared DNA less (P- 0.038) as compared to manual method (P-0.013). Also, time taken to process the samples in QIAcube was 23% less than the kit-based method.

CONCLUSION

Overall analysis of QIAcube platform suggests that it yields more better, uniform, and less-sheared quality of nucleic acid in a relatively less time as compared to manual extraction kits.

Impact of HFE-2 and HAMP Gene Variations on Iron Overload in Pediatric Patients with Non-Transfusion Dependent Thalassemia: A Pilot Study

Patients with non-transfusion dependent thalassemia (NTDT) develop variable degrees of iron overload. Possible genes which may be implicated in causing iron overload are hepcidin (HAMP) and hemojuvelin (HFE). There is variable data assessing the role of c.-582Y A > G HAMP gene and H63D hotspot in HFE-1 gene in causing iron overload, while role of HFE-2 gene is undetermined. Twenty-five patients with NTDT (≥ 10 years) were assessed for iron overload. Genetic analysis for β-globin, α-globin, HAMP, HFE-2 and C282Y and H63D hotspots in HFE-1 genes was performed. T2*MRI demonstrated elevated LIC in 48% patients. No mutations were detected in HAMP gene or HFE-1 hotspots. Four single nucleotide variations (SNV) were detected in HFE-2 gene in 4 (20%) patients, including a novel SNV, p.Gln315Arg in 2 patients in heterozygous state. This is a likely pathogenic mutation; however, in heterozygous state, it did not lead to iron overload. HAMP and HFE-2 gene variations were infrequently seen in this pilot study, with no significant impact on iron overload. Presence of SNV p.Gln315Argin HFE-2 gene needs to be evaluated in larger sample sizes in our population to determine the incidence in homozygous state and its association with iron overload.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12288-021-01442-9.

Effect of Sepsis on Iron Parameters in a Population with High Prevalence of Malnutrition and Iron Deficiency: A Cross-Sectional Case-Control Pilot Study

There is lack of data on iron metabolism in critically ill sepsis children from population with high prevalence of iron deficiency (ID). The study was designed to study impact of sepsis on iron parameters in children with ID. Sepsis patients (age 6-59 months) and their apparently healthy sibling/cousin as controls were enrolled in this case-control pilot study. Serum iron, TIBC, transferrin saturation, ferritin and sTfR were measured in the two groups. sTfR-Ferritin index was calculated. Patients (n = 134) were significantly underweight compared to controls (n = 54) (WAZ score < - 2; 58% vs. 28%; p < 0.001). Serum iron and sTfR (mg/L) were lower [71.5 (51.0, 115.0) vs. 87.0 (64.5, 130.5), p = 0.068; 3.1 (2.1, 4.5) vs. 3.5 (2.8, 4.8), p = 0.026 respectively] while serum ferritin was higher [229 (94, 484.5) vs. 22 (9.2, 51); p < 0.001] in patients compared to controls. sTfR-Ferritin index was lower in patients [1.3 (0.8, 2.3) vs. 2.5 (1.8, 4.5); p < 0.001]. ROC AUC (patients vs. controls) were 0.89 (95% CI 0.83-0.95) and 0.76 (95% CI 0.68-0.85) for ferritin and sTfR-ferritin index respectively. Survivors and non-survivors were similar in terms of iron parameters. Sepsis-induced alterations in iron parameters among ID children are complex. Qualitatively it is similar (with quantitative differences) to non-ID adult population. Lack of correlation of iron parameters with mortality may be due to ID-associated immune dysfunction.

Immunoglobulins and Lymphocyte Subsets in Children with Infantile Tremor Syndrome

In this hospital-based, cross-sectional study, immunoglobulin levels and lymphocyte subsets status were evaluated in children with infantile tremor syndrome (ITS) [neurocutaneous infantile B12 deficiency (NIB) syndrome]. Blood samples were drawn at the baseline (n = 28) and at 6 wk (n = 25) after treatment. A low IgG/IgA or IgM was more likely in untreated children than post-treatment (p = 0.0368). Low B cells were observed in 9 (36%), low T cells in 5 (20%), and low NK cells in 2 patients. T cell subset analysis showed low CD4 + helper T cells in 5 (20%) and low CD8 + cytotoxic T cells in 2 patients. Abnormally low percentage of low B cell/T cells/NK cells was more likely in untreated children than post-treatment (p = 0.0165). In conclusion, a proportion of children with ITS have changes in immunoglobulin and T cell subsets not consistent with any clearly defined immune abnormality, and not all such changes revert at 6 wk.

Clinico-Hematological Profile and Copy Number Abnormalities in a Cohort of STIL-TAL1 and NUP214-ABL1 Positive Pediatric T-Cell Acute Lymphoblastic Leukemia

T cell acute lymphoblastic leukaemia (T-ALL) is a genetically heterogeneous and aggressive form of malignancy. Although a number of recurrent fusion genes are reported in T-ALL, their involvement in disease stratification and therapeutic intervention is still controversial. Considering the prognostic value of STIL-TAL1 fusion and tyrosine kinase inhibitor (TKI) based therapeutic potential of NUP214-ABL1, the present study aimed to investigate their frequency and clinical correlation in pediatric T-ALL cases. Our cohort consisted of 48 T-ALL pediatric cases (age ≤ 12 years) with a median age of 6 years and male to female ratio of 20.5:1. The median TLC of the study group was noted to be 220,000/ cu mm with a range from 26,810/cu mm to 785,430/cu mm. By MLPA and RT-PCR analysis we observed that 11/48 cases (23%) showed STIL-TAL1 fusion and 4/48 cases (8.3%) had NUP214-ABL1 fusion gene. Both of the fusion genes did not show any significant correlation with any of the clinico-hematological or treatment outcome parameters. However, upon analysis of copy number variations (CNVs) with other clinically relevant genes, we found significant correlation between LEF1 (p = 0.024) and PTEN (p = 0.049) gene deletions with STIL/TAL1 fusion in T-ALL patients. NUP214-ABL1 fusion gene did not reveal any association with either CNVs or with survival. Although limited with the small cohort size and follow up, our study supports the similar frequency of these fusions as compared to other Asian and Western studies and also highlights utility of MLPA technique as a good diagnostic modality to screen for both STIL-TAL1 and NUP214-ABL1 fusions in a single assay with additional data on secondary copy number changes.

Assessment of the Effect of Complete Dentures on Respiratory Performance: A Spirometric Analysis

Background

Among the vital functions, respiration can be claimed to be one of the most important. A thorough understanding of the patient should be an important aspect a prosthodontist should dwell into so as to predispose patients to acknowledge the kind of prosthesis they require. Hence, the present study was conducted for assessing the effect of complete dentures on respiratory performance.

Materials and Methods

Fifty patients with the presence of complete edentulous arch and who had a history of complete denture usage for at least 5 years were enrolled. All the spirometric procedures were performed by trained technicians. A diagnostic spirometer was employed for performing the spirometric test. Testing was carried out in the following steps: Stage 1: testing in the absence of denture, Stage 2: testing in the presence of both dentures, Stage 3: testing in the presence of maxillary denture only, and Stage 4: testing in the presence of mandibular dentures only. Forced vital capacity (FVC) value, peak expiratory flow (PEF) value, forced expiratory volume in 1 s (FEV1) value, and forced expiratory flow 25%-75% (FEF_25-75) value were recorded with the spirometric test. Analysis of all the results was done by SPSS software.

Results

The spirometric value of FVC, PEF, FEV1, and FEF_25-75 in the absence of both maxillary and mandibular dentures (Stage 1) was found to be 3.18, 5.83, 2.44, and 2.80, respectively. The spirometric value of FVC, PEF, FEV1, and FEF_25-75 in the presence of both maxillary and mandibular dentures (Stage 2) was found to be 3.09, 5.67, 2.41, and 2.67, respectively. While analyzing statistically, it was seen that there was a significant decrease in the value of spirometric variables in the presence of dentures.

Conclusion

Chronic denture wearer edentulous patients are subjected to the risk of development of spirometric alterations. Hence, these patients should be given timely instructions about the various respiratory exercise protocols.

TPMT and NUDT15 polymorphisms in thiopurine induced leucopenia in inflammatory bowel disease: a prospective study from India

Background

Polymorphisms in thiopurine methyltransferase (TPMT) and Nudix hydrolase-15 (NUDT15) have been implicated as the predominant cause of thiopurine induced leukopenia in the Western countries and East Asia respectively. Exact role of these polymorphisms in South Asian population with inflammatory bowel disease (IBD) is uncertain.

Methods

We included consecutive patients with IBD who were initiated on thiopurines at a center in North India. The dosage of thiopurines was titrated using regular monitoring of hemogram and liver function tests. Three TPMT polymorphisms (c.238 G > C, c.460 G > A, and c.719A > G) and one NUDT15 polymorphism (c.415 C > T) were assessed. Comparison regarding incidence of leukopenia and maximum tolerated thiopurine dosage was performed between those with wild polymorphism and those with TPMT and NUDT15 polymorphisms, respectively.

Results

Of the 119 patients (61 males, mean age 36.8 ± 13.5 years), 105 (88.2%) had ulcerative colitis and 14 (11.8%) had Crohn’s disease. Leukopenia was noted in 33 (27.7%), gastrointestinal intolerance in 5 (4.2%) and pancreatitis in 2 (1.6%). TPMT polymorphisms were detected amongst five patients of whom 1 developed leukopenia. NUDT15 polymorphism was noted in 13 patients of whom 7 had leukopenia. The odds of developing leukopenia in TPMT polymorphism were non-significant (0.77, 95% CI:0.0822 to 7.2134, P = 0.819) but were significantly higher in those with NUDT15 polymorphism (3.5933, 1.1041 to 11.6951, P value: = 0.0336).

Conclusion

NUDT15 polymorphism was more frequent than TPMT polymorphisms and was associated with thiopurine induced leukopenia. However, the tested polymorphisms account for only 24.2% of the risk of thiopurine induced leukopenia.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12876-021-01900-8.

Effective Downregulation of BCR-ABL Tumorigenicity by RNA Targeted CRISPR-Cas13a

AIM

To induce BCR-ABL gene silencing using CRISPR Cas13a.

BACKGROUND

CML is a clonal myeloproliferative disorder of pluripotent stem cells driven by a reciprocal translocation between chromosomes 9 and 22 forming a BCR-ABL fusion gene. Tyrosine- kinase inhibitor drugs like imatinib are the mainstay of treatment and cases resistant to these drugs have a poor prognosis in the absence of a compatible stem-cell donor. However with rapid advancements in gene-editing technologies most studies are now focusing on developing a translational model targeting single-gene disorders with a prospective permanent cure.

OBJECTIVE

To explore the potential application of the RNA targeting CRISPR-Cas13a system for effective knockdown of BCR-ABL fusion transcript in a CML cell line K562.

METHODS

CRISPR Cas13a crRNA was designed specific to the chimeric BCR-ABL gene and the system was transfected as a two-plasmid system into a CML cell line K562. The effects were enumerated by evaluating the expression levels of downstream genes dependent on the expression of the BCR-ABL gene. Also next-generation sequencing was used to ascertain the effects of CRISPR on the gene.

RESULTS

The CRISPR system was successfully able to lower the expression of downstream genes [pCRKL and pCRK] dependent on the activated BCR-ABL kinase signal by up-to 4.3 folds. The viability of the CRISPR-treated cells was also significantly lowered by 373.83-fold [p-value= 0.000891196]. The time-dependent kinetics also highlighted the significant in-vitro suppressive activity to last up to 8 weeks [p-value: 0.025]. As per the cDNA sequencing data from the Oxford MinION next-generation sequencer the CRISPR treated cells show 62.37% suspected cleaved reads.

CONCLUSION

These preliminary results highlight an excellent potential application of RNA targeting CRISPRs in Haematological neoplasms like CML and should pave the way for further research in this direction.

De novo double-hit B-cell precursor leukemia/lymphoma - an unusual presentation as peritoneal lymphomatosis

Peritoneal lymphomatosis (PL) is a rare presentation of extranodal precursor leukemia/lymphoma. The presentation is often non-specific, leading to delayed diagnosis and treatment. In this case, though the preliminary diagnosis was established on ascitic fluid cytology, the disease progressed rapidly, leading to demise before initiating chemotherapy. Immunophenotyping and molecular studies, performed later, established a diagnosis of de novo B-cell precursor leukemia/lymphoma with MYC, BCL2 rearrangements (Double-hit lymphoma). MYC, BCL2 rearrangements are rarely reported in precursor B-lymphoma/leukemia which carry dismal prognosis. In this report, we illustrate autopsy findings of PL in an elderly gentleman who presented with ascites for evaluation.

Wiskott Aldrich Syndrome: A Multi-Institutional Experience From India

Background

Wiskott Aldrich syndrome (WAS) is characterized by bleeding manifestations, recurrent infections, eczema, autoimmunity, and malignancy. Over the last decade, improved awareness and better in-house diagnostic facilities at several centers in India has resulted in increased recognition of WAS. This study reports collated data across major primary immunodeficiency diseases (PID) centers in India that are involved in care of children with WAS and highlights the varied clinical presentations, genetic profile, and outcomes of patients in India.

Methods

Request to share data was sent to multiple centers in India that are involved in care and management of patients with PID. Six centers provided requisite data that were compiled and analyzed.

Results

In this multi-institutional cohort, clinical details of 108 patients who had a provisional diagnosis of WAS were received. Of these, 95 patients with 'definite WAS' were included Fourteen patients were classified as XLT and 81 patients as WAS. Median age at onset of symptoms of patients was 3 months (IQR 1.6, 6.0 months) and median age at diagnosis was 12 months (IQR 6,48 months). Clinical profile included bleeding episodes (92.6%), infections (84.2%), eczema (78.9%), various autoimmune manifestations (40%), and malignancy (2.1%). DNA analysis revealed 47 variants in 67 cases. Nonsense and missense variants were the most common (28.4% each), followed by small deletions (19.4%), and splice site defects (16.4%). We also report 24 novel variants, most of these being frameshift and nonsense mutations resulting in premature termination of protein synthesis. Prophylactic intravenous immunoglobulin (IVIg) was initiated in 52 patients (54.7%). Hematopoietic stem cell transplantation (HSCT) was carried out in 25 patients (26.3%). Of those transplanted, disease-free survival was seen in 15 patients (60%). Transplant related mortality was 36%. Outcome details were available for 89 patients. Of these, 37% had died till the time of this analysis. Median duration of follow-up was 36 months (range 2 weeks- 12 years; IQR 16.2 months- 70 months).

Conclusions

We report the first nationwide cohort of patients with WAS from India. Bleeding episodes and infections are common manifestations. Mortality continues to be high as curative therapy is not accessible to most of our patients.

A case series highlighting structured hematological, biochemical and molecular approach to clinical oral iron refractoriness in children: A pressing need for a 3-tier system for classification of variants in TMPRSS6 gene

In current study, we discuss clinical oral iron refractoriness cases and highlight need for a classification system to define TMPRSS6 gene variants. Out of 231 cases of microcytic hypochromic anemia screened (Sept 2019-Dec 2020), 17 cases (7.35%) with unexplained iron refractoriness (URIDA) phenotype were enrolled after ruling out secondary causes and compliance related issues. 11 (65%) had absent/negligible response (0-0.4 g/dl Hb rise) while 6 (35%) partial (0.5-0.9 g/dl Hb rise) response to initial iron trial at 4-8 weeks. Of these 17 cases, inappropriate hepcidin levels (normal-high) were noted in 11/15 (73%) tested. TSAT/Hepcidin ratio was low in 13/15 (87%). Genetic analysis of TMPRSS6 gene by NGS revealed variations in 15/17 (88%) cases. 10/15 cases with variations harbored a common splice site INDEL that was noted to be pathogenic SNP (MAF-0.19) on case-control association study in combination with other known missense SNPs with an odds ratio of 6.38 and relative risk 2.66 (p- < 0.01).

Prevalence of polymorphisms in thiopurine metabolism and association with adverse outcomes: a South Asian region-specific systematic review and meta-analysis

Background: Prevalence and impact of thiopurine S-methyltransferase (TPMT) and Nudix hydrolase (NUDT15) minor allele frequencies in South Asian population is unclear.Methods: We searched PubMed and Embase with keywords-TPMT and NUDT15 combined with South Asian countries. We included studies reporting frequency of TPMT and NUDT15 polymorphisms. We estimated the pooled prevalence of TPMT and NUDT15 polymorphisms and their impact on pooled odds ratio of adverse events with thiopurines.Results: We included 26 studies in our analysis. The pooled prevalence of NUDT15 and TPMT polymorphisms was 16.5% (95% CI: 13.09-20.58) and 4.57% (95% CI: 3.66-5.68), respectively. In patients with adverse effects, the pooled prevalence of NUDT15 and TPMT polymorphism was 49.51% (95% C.I. 21.69-77.64) and 9.47% (95% C.I. 5.39-16.11), respectively. The odds ratio (OR) of adverse events with presence of TPMT polymorphisms was 3.65 (95% C.I., 1.43-9.28). The pooled OR for adverse events in presence of NUDT15 polymorphism was 12.63 (95% C.I., 3.68-43.26).Conclusion: NUDT15 were reported more frequently than the TPMT polymorphisms in South Asian population and were more frequently associated with adverse events. These findings may have implications for preemptive testing amongst South Asian population and immigrants prior to starting thiopurines.

A Case of Novel GATA-1 Mutation-positive Transient Abnormal Myelopoiesis With Life-threatening Complications in a Neonate With Down Syndrome

Transient abnormal myelopoiesis is a transient myeloproliferative disorder seen in ∼15% to 20% of infants with Down syndrome. These infants are usually asymptomatic, requiring only monitoring, but they can have variable severity of symptoms up to multisystemic dysfunction requiring chemotherapy. GATA-1 somatic mutations acquired in utero are pathognomic of this entity and present nearly in all cases. Herein, we present a case of Down syndrome in a neonate who presented within her first week of life with life-threatening features of transient abnormal myelopoiesis requiring chemotherapy support. In addition, next-generation sequencing revealed a small mutant clone (8%) positive for a novel frameshift GATA-1 mutation.

Hyperferritinemia in children hospitalized with scrub typhus

BACKGROUND

Hyperferritinemia is increasingly associated with mortality in sepsis. Studies estimating the prevalence of hyperferritinemia in pediatric scrub typhus are limited.

METHODS

This was a secondary analysis of a prospective observational study (FERRIS) from a tertiary care teaching hospital in North India where 72 children with confirmed scrub typhus, 4 (5.5%) PCR positive, 55 (76.4%)-IgM ELISA positive, and 13 (18.1%)-both PCR and ELISA positive, were analyzed. Serum ferritin was measured in 62 children to identify the prevalence of hyperferritinemia and determine its association with mortality.

RESULTS

Hyperferritinemia (> 500 μg/L) was seen in 72.6% [n = 45] children; 26 (41.9%) were mild (500-2000 μg/L), 13 (21%) were moderate (2000-10,000 μg/L), and 6 (9.7%) were severe (> 10,000 μg/L). Early presentation to hospital (≤ 7 days of febrile illness) had more survivors than late presentation (> 7 days). Non-survivors had significantly higher PRISM III, PELOD-2, hyperlactatemia, hypoalbuminemia, organ dysfunction, need for mechanical ventilation, and need of RRT. Ferritin had poor sensitivity and specificity in predicting survival with AUC of 0.56. Organ dysfunction and risk scores as PRISM III, PELOD 2, and VIS at admission were better predictors with AUC (95% CI) of 0.72 (0.56, 0.89), 0.77 (0.63, 0.92), and 0.90 (0.78, 1.0) respectively.

CONCLUSIONS

Hyperferritinemia is common in scrub typhus but it did not predict survival. Organ dysfunction and risk scores were better predictors of mortality than ferritin.

Epigenetic analysis reveals significant differential expression of miR-378C and miR-128-2-5p in a cohort of relapsed pediatric B-acute lymphoblastic leukemia cases

INTRODUCTION AND OBJECTIVE

Epigenetic changes play a major role in mediating chemoresistance and relapse in pediatric ALL, and hence in current pilot study, we tried to identify DNA methylation, miRNA expression, and copy number variations (CNVs) in a cohort of relapse pediatric B-ALL cases.

METHODOLOGY

DNA methylation, miRNA expression, and CNV analysis were performed in a total of 14, 16, and 18 cases as diagnosis-relapse samples. Briefly, DNA methylation was performed using Infinium HumanMethylation850 chip and data analyzed using RnBeads. miRNA was sequenced on illumina NextSeq500 platform for 20M 75bp SE reads and analyzed by DESeq2. CNVs were assessed by MLPA assay using the ALL P-335 probemix kit and analyzed by coffalyzer.net.

RESULTS

On methylation analysis, oncogenes MYCN, MYB, and EGFR and tumor suppressor genes MDM4 & BCL11B were found differentially expressed as compared to controls (p-0.03). In addition, protooncogenes-AXL, HCK, MED12, and ETS2-were hypomethylated/overexpressed in 4 or more cases (P < .05). miRNA analysis revealed significant differential expression of miR-128-2-5p and miR-378C (p-4.4e-15 and p-6.4E-12) in relapse samples. CNV analysis revealed that frequency of good and intermediate/poor risk CNV profile at diagnosis was nearly equal (40% vs 60%). However, CDKN2A/2B and IKZF1 gene CNVs if present in initial diagnostic clone usually persisted in relapse clone.

DISCUSSION AND CONCLUSION

Our pilot study highlights two miRNAs (miR-128-2-5p and miR-378C) as possible candidate biomarkers of relapsed B-ALL. However, these miRNAs and hypomethylated protooncogene signature noted in our data needs validation in a larger series of B-ALL.

Deficiency of Adenosine Deaminase 2 in Adults and Children: Experience From India

OBJECTIVE

Deficiency of adenosine deaminase 2 (DADA2) is a potentially fatal monogenic syndrome characterized by variable manifestations of systemic vasculitis, bone marrow failure, and immunodeficiency. Most cases are diagnosed by pediatric care providers, given the typical early age of disease onset. This study was undertaken to describe the clinical phenotypes and treatment response both in adults and in children with DADA2 in India.

METHODS

A retrospective analysis of pediatric and adult patients with DADA2 diagnosed at various rheumatology centers across India was conducted. Clinical characteristics, diagnostic findings, and treatment responses were analyzed in all subjects.

RESULTS

In total, 33 cases of DADA2 were confirmed in this cohort between April 2017 and March 2020. Unlike previous studies, nearly one-half of the confirmed cases presented during adulthood. All symptomatic patients exhibited features of vasculitis, whereas constitutional symptoms and anemia were more common in pediatric patients. Cutaneous and neurologic involvement were common, and 18 subjects had experienced at least one stroke. In addition, the clinical spectrum of DADA2 was expanded by recognition of novel features in these patients, including pancreatic infarction, focal myocarditis, and diffuse alveolar hemorrhage. Treatment with tumor necrosis factor inhibitors (TNFi) was initiated in 25 patients. All of the identified disease manifestations showed marked improvement after initiation of TNFi, and disease remission was achieved in 19 patients. Two cases were complicated by tuberculosis infection, and 2 deaths were reported.

CONCLUSION

This report presents the first case series of patients with DADA2 from India, diagnosed by adult and pediatric care providers. The findings raise awareness of this syndrome, particularly with regard to its presentation in adults.