Browsing by Author "Laxmi Kirola"

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A novel leaky splice variant in centromere protein J (CENPJ)-associated Seckel syndrome
(John Wiley and Sons Inc, 2022) Navneesh Yadav; Laxmi Kirola; Thenral S Geetha; Kirti Mittal; Jayarama Kadandale; Yuval Yogev; Ohad S. Birk; Neerja Gupta; Prahlad Balakrishnan; Manisha Jana; Meena Gupta; Madhulika Kabra; Bittianda Kuttapa Thelma
Abstract: Primary microcephaly and Seckel syndrome are rare genetically and clinically heterogenous brain development disorders. Several exonic/splicing mutations are reported for these disorders to date, but ∼40% of all cases remain unexplained. We aimed to uncover the genetic correlate(s) in a family of multiple siblings with microcephaly. A novel homozygous intronic variant (NC_000013.10:g.25459823T>C) in CENPJ (13q12) segregating with all four affected male siblings was identified by exome sequencing and validated by targeted linkage approach (logarithm of the odds score 1.8 at θ 0.0). RT-PCR of CENPJ in affected siblings using their EBV derived cell lines showed aberrant transcripts suggestive of exon skipping confirmed by Sanger sequencing. Significantly reduced wild type transcript/protein in the affected siblings having the splice variant indicates a leaky gene expression of pathological relevance. Based on known CENPJ function, assessing for mitotic alterations revealed defect in centrosome duplication causing mono/multicentrosome(s) at prophase, delayed metaphase, and unequal chromosomal segregation in patient cells. Clinical features witnessed in this study expand the spectrum of CENPJ-associated primary microcephaly and Seckel syndrome. Furthermore, besides the importance of regulatory variants in classical monogenic disorders these findings provide new insights into splice site biology with possible implications for ASO-based therapies. © 2022 John Wiley & Sons Ltd/University College London.
Gene Regulation, DNA and RNA Structure and Sequencing
(CRC Press, 2023) Neetu Verma; Deepa Bhatt; Laxmi Kirola
During the growth and development of an organism, gene regulation plays an essential role in the expression and regulation of genes in a spatiotemporal manner. This can be regulated either at the transcriptional level or at the translational level via transcriptional and translational machinery, respectively. In addition, post-translational modifications along with regulatory noncoding RNAs can also control gene expression through a variety of factors and regulators. A gene is a sequence of nucleotides in the DNA that conveys information from cell to cell and from generation to generation. The DNA molecules are transcribed primarily into RNA molecules (mRNA, tRNA, and rRNA), and the mRNA carries information stored in the DNA by translating it into functional proteins. To better understand such mechanisms, new bioinformatic tools, algorithms, and databases have been developed and used on a cloud computing platform. High-throughput sequencing technologies (DNA, RNA, protein, etc.) have evolved the bioinformatic tools for studying gene expression and regulation in almost all organisms, including bacteria, plants, and animals. This has significantly improved the routine practice of drug discovery, medicine, science, and technology. This chapter introduces gene regulation, DNA and RNA biology, the algorithms, and bioinformatic tools involved in these processes, and the latest breakthroughs in bioinformatics and sequencing. © 2023 CRC Press.
Identification and molecular characterization of two recurrent missense mutations in the RS1 gene in two families with X-linked retinoschisis from North India
(John Wiley and Sons Inc, 2023) Souradip Chatterjee; Shashank Gupta; Laxmi Kirola; Abhishek Chandra; Ashim Mukherjee; Mousumi Mutsuddi
X-linked retinoschisis (XLR) is a rare medical condition that involves in the splitting of neurosensory layers and the impairment of vision in the retina. In majority of the XLR cases, pathogenic variants in Retinoschisin 1 (RS1) gene have been implicated in males with an early age of onset during early childhood. In the present study, we have recruited two North Indian families having multiple affected male members, who were diagnosed with XLR. The entire protein-coding region of RS1 was screened by PCR-Sanger sequencing and two recurrent pathogenic variants (p.I81N and p.R102Q) were unraveled. The in vitro study of these variants demonstrated the aggregation of mutant RS1 within the endoplasmic reticulum. Furthermore, mutant forms of this protein showed significant intracellular retention, which was evident by the absence of retinoschisin protein fractions in the extracellular media. These inferences were also supported by extensive bioinformatics analysis of the mutants, which showed dramatic conformational changes in the local structure of retinoschisin. Thus, our study suggests that the identified pathogenic variants interfere with proper protein folding, leading to anomalous structural changes ultimately resulting in intracellular retention of retinoschisin within the retina. © 2023 Wiley Periodicals LLC.
Identification of a compound heterozygous mutation in GDAP1 gene in a consanguineous South Indian family with Charcot–Marie–Tooth (CMT) Disease
(Springer Nature, 2025) Laxmi Kirola; Deepika Srivastava Joshi; Souradip Chatterjee; Madhusudan Tapadia; Ashim Mukherjee; M. Mutsuddi
Background: Charcot–Marie–Tooth (CMT) is a clinically, electro-physiologically, and genetically heterogenous group of muscle disease which is also known as hereditary motor and sensory neuropathy. Autosomal recessive forms of CMT type 4A have been reported with either homozygous or compound heterozygous mutations in a gene that encodes ganglioside-induced differentiation-associated protein-1 (GDAP1). GDAP1 is located on 8q21, and plays a major role in ganglioside differentiation and Schwann cell function, as well as regulates neuronal and axonal development. Case presentation: In this study, we recruited a consanguineous south Indian family with an affected patient, an unaffected sibling, and the mother. The patient was affected with progressive weakness in the lower and upper limbs, atrophy of small muscles of the foot and hands, club shaped hands, steppage gait, hoarseness, and decreased muscle tone. His nerve biopsy examination revealed peripheral nerve demyelination and nerve conduction testing confirmed a reduction in nerve activities, while MRI showed mild degenerative changes in the cervical spine. Further, targeted exome sequencing (TES) and copy number variation analysis were performed on the patient. TES identified a compound heterozygous mutation that includes a missense mutation and a 3’UTR mutation (NM_018972.4: c.413A > G:p.His138Arg; g.74488790C > A:c.*29C > A, respectively) in GDAP1. The missense change is not reported in available public databases, while the UTR variant is seen only in the South Asian population in gnomAD (allele frequency = 0.00002). Multiple in silico prediction tools show that the missense mutation is damaging. Subsequently, in silico protein modeling, phylogenetic conservation analysis, and the impact of the mutation on the canonical transcript have also been performed. The compound heterozygous mutation was confirmed in the patient by PCR-Sanger sequencing and was shown to segregate within the family. Conclusions: The combined results support the fact that these two mutations in GDAP1 link the genotype–phenotype correlation in the family. This will help the family in genetic testing, counseling, and early diagnosis. Our findings support expanded phenotypic characterization along with the genetic spectrum of GDAP1 mutations in CMT type4A in the Indian population. © The Author(s) 2025.
Recent Updates on the Genetics of Amyotrophic Lateral Sclerosis and Frontotemporal Dementia
(Springer, 2022) Laxmi Kirola; Ashim Mukherjee; Mousumi Mutsuddi
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) primarily affect the motor and frontotemporal areas of the brain, respectively. These disorders share clinical, genetic, and pathological similarities, and approximately 10–15% of ALS-FTD cases are considered to be multisystemic. ALS-FTD overlaps have been linked to families carrying an expansion in the intron of C9orf72 along with inclusions of TDP-43 in the brain. Other overlapping genes (VCP, FUS, SQSTM1, TBK1, CHCHD10) are also involved in similar functions that include RNA processing, autophagy, proteasome response, protein aggregation, and intracellular trafficking. Recent advances in genome sequencing have identified new genes that are involved in these disorders (TBK1, CCNF, GLT8D1, KIF5A, NEK1, C21orf2, TBP, CTSF, MFSD8, DNAJC7). Additional risk factors and modifiers have been also identified in genome-wide association studies and array-based studies. However, the newly identified genes show higher disease frequencies in combination with known genes that are implicated in pathogenesis, thus indicating probable digenetic/polygenic inheritance models, along with epistatic interactions. Studies suggest that these genes play a pleiotropic effect on ALS-FTD and other diseases such as Alzheimer’s disease, Ataxia, and Parkinsonism. Besides, there have been numerous improvements in the genotype–phenotype correlations as well as clinical trials on stem cell and gene-based therapies. This review discusses the possible genetic models of ALS and FTD, the latest therapeutics, and signaling pathways involved in ALS-FTD. © 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.