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Article ; Online: Insights into the mechanism of

Mahant, Sheefali / Sahajpal, Nikhil S / Nanda, Sanju

2021 Volume 16, Page(s) 1181–1193

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Acne Vulgaris/drug therapy ; Anti-Bacterial Agents/pharmacology ; Cymbopogon/chemistry ; Humans ; Microbial Sensitivity Tests ; Oils, Volatile/pharmacology ; Plant Oils/pharmacology ; Propionibacteriaceae/drug effects
Chemical Substances	Anti-Bacterial Agents ; Oils, Volatile ; Plant Oils
Language	English
Publishing date	2021-10-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2254620-0
ISSN	1746-0921 ; 1746-0913
ISSN (online)	1746-0921
ISSN	1746-0913
DOI	10.2217/fmb-2021-0039
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Article ; Online: Immune Factors Drive Expression of SARS-CoV-2 Receptor Genes Amid Sexual Disparity.

Vashisht, Ashutosh / Ahluwalia, Pankaj / Mondal, Ashis K / Singh, Harmanpreet / Sahajpal, Nikhil S / Fulzele, Sadanand / Kota, Vamsi / Gahlay, Gagandeep K / Kolhe, Ravindra

Viruses

2023 Volume 15, Issue 3

Abstract: The emergence of COVID-19 has led to significant morbidity and mortality, with around seven million deaths worldwide as of February 2023. There are several risk factors such as age and sex that are associated with the development of severe symptoms due ... ...

Abstract	The emergence of COVID-19 has led to significant morbidity and mortality, with around seven million deaths worldwide as of February 2023. There are several risk factors such as age and sex that are associated with the development of severe symptoms due to COVID-19. There have been limited studies that have explored the role of sex differences in SARS-CoV-2 infection. As a result, there is an urgent need to identify molecular features associated with sex and COVID-19 pathogenesis to develop more effective interventions to combat the ongoing pandemic. To address this gap, we explored sex-specific molecular factors in both mouse and human datasets. The host immune targets such as TLR7, IRF7, IRF5, and IL6, which are involved in the immune response against viral infections, and the sex-specific targets such as AR and ESSR were taken to investigate any possible link with the SARS-CoV-2 host receptors ACE2 and TMPRSS2. For the mouse analysis, a single-cell RNA sequencing dataset was used, while bulk RNA-Seq datasets were used to analyze the human clinical data. Additional databases such as the Database of Transcription Start Sites (DBTS), STRING-DB, and the Swiss Regulon Portal were used for further analysis. We identified a 6-gene signature that showed differential expression in males and females. Additionally, this gene signature showed potential prognostic utility by differentiating ICU patients from non-ICU patients due to COVID-19. Our study highlights the importance of assessing sex differences in SARS-CoV-2 infection, which can assist in the optimal treatment and better vaccination strategies.
MeSH term(s)	Humans ; Female ; Male ; Animals ; Mice ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; COVID-19/genetics ; Peptidyl-Dipeptidase A/metabolism ; Angiotensin-Converting Enzyme 2/genetics ; Angiotensin-Converting Enzyme 2/metabolism ; Immunologic Factors ; Interferon Regulatory Factors/metabolism
Chemical Substances	Peptidyl-Dipeptidase A (EC 3.4.15.1) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Immunologic Factors ; Irf5 protein, mouse ; Interferon Regulatory Factors
Language	English
Publishing date	2023-02-28
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15030657
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Article ; Online: Gene signatures with therapeutic value: emerging perspective for personalized immunotherapy in renal cancer.

Ahluwalia, Pankaj / Mondal, Ashis K / Sahajpal, Nikhil S / Rojiani, Mumtaz V / Kolhe, Ravindra

Immunotherapy

2021 Volume 13, Issue 18, Page(s) 1535–1547

Abstract: Renal cancer is one of the deadliest urogenital diseases. In recent years, the advent of immunotherapy has led to significant improvement in the management of patients with renal cancer. Although cancer immunotherapy and its combinations had benefited ... ...

Abstract	Renal cancer is one of the deadliest urogenital diseases. In recent years, the advent of immunotherapy has led to significant improvement in the management of patients with renal cancer. Although cancer immunotherapy and its combinations had benefited numerous patients, several challenges need to be addressed. Apart from the high costs of treatment, the lack of predictive biomarkers and toxic side-effects have impeded its wider applicability. To address these issues, new biomarkers are required to predict responsiveness and design personalized treatment strategies. Recent advances in the field of single-cell sequencing and multi-dimensional spatial transcriptomics have identified clinically relevant subtypes of renal cancer. Furthermore, there is emerging potential for gene signatures based on immune cells, non-coding RNAs, and pathways such as metabolism and RNA modification. In this review article, we have discussed recent progress in the identification of gene signatures with predictive and prognostic potential in renal cancer.
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Humans ; Kidney Neoplasms/genetics ; Kidney Neoplasms/metabolism ; Kidney Neoplasms/therapy ; Precision Medicine ; RNA-Seq ; Single-Cell Analysis
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2021-11-10
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2495964-9
ISSN	1750-7448 ; 1750-743X
ISSN (online)	1750-7448
ISSN	1750-743X
DOI	10.2217/imt-2021-0187
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Article ; Online: A framework for the clinical implementation of optical genome mapping in hematologic malignancies.

Levy, Brynn / Kanagal-Shamanna, Rashmi / Sahajpal, Nikhil S / Neveling, Kornelia / Rack, Katrina / Dewaele, Barbara / Olde Weghuis, Daniel / Stevens-Kroef, Marian / Puiggros, Anna / Mallo, Mar / Clifford, Benjamin / Mantere, Tuomo / Hoischen, Alexander / Espinet, Blanca / Kolhe, Ravindra / Solé, Francesc / Raca, Gordana / Smith, Adam C

American journal of hematology

2024 Volume 99, Issue 4, Page(s) 642–661

Abstract: Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional ... ...

Abstract	Optical Genome Mapping (OGM) is rapidly emerging as an exciting cytogenomic technology both for research and clinical purposes. In the last 2 years alone, multiple studies have demonstrated that OGM not only matches the diagnostic scope of conventional standard of care cytogenomic clinical testing but it also adds significant new information in certain cases. Since OGM consolidates the diagnostic benefits of multiple costly and laborious tests (e.g., karyotyping, fluorescence in situ hybridization, and chromosomal microarrays) in a single cost-effective assay, many clinical laboratories have started to consider utilizing OGM. In 2021, an international working group of early adopters of OGM who are experienced with routine clinical cytogenomic testing in patients with hematological neoplasms formed a consortium (International Consortium for OGM in Hematologic Malignancies, henceforth "the Consortium") to create a consensus framework for implementation of OGM in a clinical setting. The focus of the Consortium is to provide guidance for laboratories implementing OGM in three specific areas: validation, quality control and analysis and interpretation of variants. Since OGM is a complex technology with many variables, we felt that by consolidating our collective experience, we could provide a practical and useful tool for uniform implementation of OGM in hematologic malignancies with the ultimate goal of achieving globally accepted standards.
MeSH term(s)	Humans ; In Situ Hybridization, Fluorescence ; Hematologic Neoplasms/diagnosis ; Hematologic Neoplasms/genetics ; Karyotyping ; Chromosome Mapping
Language	English
Publishing date	2024-01-02
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	196767-8
ISSN	1096-8652 ; 0361-8609
ISSN (online)	1096-8652
ISSN	0361-8609
DOI	10.1002/ajh.27175
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Article ; Online: Molecular Remodeling of the Insulin Receptor Pathway by Thiazolidinediones in Type 2 Diabetes Mellitus: A Brief Review.

Sahajpal, Nikhil S / Jain, Subheet K

Protein and peptide letters

2016 Volume 23, Issue 9, Page(s) 836–847

Abstract: ... effect(s). The TZD's are not only PPARγ agonists, but substantial insulin sensitizing activity is ... to its overall performance. TZD's alter(s) cell response via downstream players, primarily IRS, Akt/PKB, PKC ... GLUT4, MEK, ERK and transcription factor PGC1α. Thus, this review will focus on the alteration(s ...

Abstract	Type 2 diabetes mellitus (T2DM) is characterized by abnormalities in carbohydrate, lipoprotein and lipid metabolism, leading to hyperglycemia and several other complications. Insulin is the major hormone regulating these facets by eliciting various biological responses through its receptor. Insulin exerts diverse effects on cells by targeting distinct functions such as gene expression, fatty acid synthesis, glucose transport and receptor translocation. Insulin mediates these effects through signaling pathways utilizing adapter molecules like small Gproteins, lipid and tyrosine kinases. The anomalous cell response in diabetic condition is due to altered expression/function of these molecules. Thiazolidinediones (TZD's), a class of oral hypoglycemic drugs, have shown to modify these responses, leading to insulin sensitizing effect(s). The TZD's are not only PPARγ agonists, but substantial insulin sensitizing activity is observed through its direct and indirect targets of the insulin receptor pathway, which contributes to its overall performance. TZD's alter(s) cell response via downstream players, primarily IRS, Akt/PKB, PKC, GLUT4, MEK, ERK and transcription factor PGC1α. Thus, this review will focus on the alteration(s) of these molecules in various cell types in diabetic condition and their regulation by TZD's. The physiological changes that occur at the molecular level in T2DM and their modulation by TZD's will provide insights into the key players involved and the potential drug targets for future drug development. The review further highlights the key markers to be evaluated in screening of any potential anti-diabetic agent, and to standardize therapy for T2DM based upon its modulation of the various signaling pathways.
MeSH term(s)	Animals ; Antigens, CD/chemistry ; Antigens, CD/metabolism ; Diabetes Mellitus, Type 2/drug therapy ; Diabetes Mellitus, Type 2/metabolism ; Drug Evaluation, Preclinical ; Gene Expression Regulation/drug effects ; Humans ; Hypoglycemic Agents/pharmacology ; Insulin/metabolism ; Receptor, Insulin/chemistry ; Receptor, Insulin/metabolism ; Signal Transduction/drug effects ; Thiazolidinediones/pharmacology ; Thiazolidinediones/therapeutic use
Chemical Substances	Antigens, CD ; Hypoglycemic Agents ; Insulin ; Thiazolidinediones ; INSR protein, human (EC 2.7.10.1) ; Receptor, Insulin (EC 2.7.10.1)
Language	English
Publishing date	2016-06-09
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	1280776-x
ISSN	1875-5305 ; 0929-8665
ISSN (online)	1875-5305
ISSN	0929-8665
DOI	10.2174/0929866523666160703183541
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Zs.A 4452: Show issues

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Article ; Online: Multisite Assessment of Optical Genome Mapping for Analysis of Structural Variants in Constitutional Postnatal Cases.

Iqbal, M Anwar / Broeckel, Ulrich / Levy, Brynn / Skinner, Steven / Sahajpal, Nikhil S / Rodriguez, Vanessa / Stence, Aaron / Awayda, Kamel / Scharer, Gunter / Skinner, Cindy / Stevenson, Roger / Bossler, Aaron / Nagy, Peter L / Kolhe, Ravindra

The Journal of molecular diagnostics : JMD

2023 Volume 25, Issue 3, Page(s) 175–188

Abstract: This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected ... ...

Abstract	This study compares optical genome mapping (OGM) performed at multiple sites with current standard-of-care (SOC) methods used in clinical cytogenetics. This study included 50 negative controls and 359 samples from individuals (patients) with suspected genetic conditions referred for cytogenetic testing. OGM was performed using the Saphyr system and Bionano Access software version 1.7. Structural variants, including copy number variants, aneuploidy, and regions of homozygosity, were detected and classified according to American College of Medical Genetics and Genomics guidelines. Repeated expansions in FMR1 and contractions in facioscapulohumeral dystrophy 1 were also analyzed. OGM results were compared with SOC for technical concordance, clinical classification concordance, intrasite and intersite reproducibility, and ability to provide additional, clinically relevant information. Across five testing sites, 98.8% (404/409) of samples yielded successful OGM data for analysis and interpretation. Overall, technical concordance for OGM to detect previously reported SOC results was 99.5% (399/401). The blinded analysis and variant classification agreement between SOC and OGM was 97.6% (364/373). Replicate analysis of 130 structural variations was 100% concordant. On the basis of this demonstration of the analytic validity and clinical utility of OGM by this multisite assessment, the authors recommend this technology as an alternative to existing SOC tests for rapid detection and diagnosis in postnatal constitutional disorders.
MeSH term(s)	Humans ; Reproducibility of Results ; Aneuploidy ; Genomics ; Cytogenetics ; Chromosome Mapping ; Fragile X Mental Retardation Protein
Chemical Substances	FMR1 protein, human ; Fragile X Mental Retardation Protein (139135-51-6)
Language	English
Publishing date	2023-02-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2022.12.005
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Zs.A 5146: Show issues

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Article ; Online: Rare structural variants, aneuploidies, and mosaicism in individuals with Mullerian aplasia detected by optical genome mapping.

Brakta, Soumia / Hawkins, Zoe A / Sahajpal, Nikhil / Seman, Natalie / Kira, Dina / Chorich, Lynn P / Kim, Hyung-Goo / Xu, Hongyan / Phillips, John A / Kolhe, Ravindra / Layman, Lawrence C

Human genetics

2023 Volume 142, Issue 4, Page(s) 483–494

Abstract: ... of copy number variants have been reported, but causal gene(s) remain to be identified. We hypothesized ...

Abstract	The molecular basis of Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome remains largely unknown. Pathogenic variants in WNT4 and HNF1B have been confirmed in a small percent of individuals. A variety of copy number variants have been reported, but causal gene(s) remain to be identified. We hypothesized that rare structural variants (SVs) would be present in some individuals with MRKH, which could explain the genetic basis of the syndrome. Large molecular weight DNA was extracted from lymphoblastoid cells from 87 individuals with MRKH and available parents. Optical genome mapping (OGM) was performed to identify SVs, which were confirmed by another method (quantitative PCR, chromosomal microarray, karyotype, or fluorescent in situ hybridization) when possible. Thirty-four SVs that overlapped coding regions of genes with potential involvement in MRKH were identified, 14 of which were confirmed by a second method. These 14 SVs were present in 17/87 (19.5%) of probands with MRKH and included seven deletions, three duplications, one new translocation in 5/50 cells-t(7;14)(q32;q32), confirmation of a previously identified translocation-t(3;16)(p22.3;p13.3), and two aneuploidies. Of interest, three cases of mosaicism (3.4% of probands) were identified-25% mosaicism for trisomy 12, 45,X(75%)/46,XX (25%), and 10% mosaicism for a 7;14 translocation. Our study constitutes the first systematic investigation of SVs by OGM in individuals with MRKH. We propose that OGM is a promising method that enables a comprehensive investigation of a variety of SVs in a single assay including cryptic translocations and mosaic aneuploidies. These observations suggest that mosaicism could play a role in the genesis of MRKH.
MeSH term(s)	Humans ; Mosaicism ; In Situ Hybridization, Fluorescence ; Aneuploidy ; Chromosome Mapping ; Congenital Abnormalities/genetics
Language	English
Publishing date	2023-02-17
Publishing country	Germany
Document type	Journal Article
ZDB-ID	223009-4
ISSN	1432-1203 ; 0340-6717
ISSN (online)	1432-1203
ISSN	0340-6717
DOI	10.1007/s00439-023-02522-8
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Article ; Online: Clinical Validation and Diagnostic Utility of Optical Genome Mapping in Prenatal Diagnostic Testing.

Sahajpal, Nikhil S / Mondal, Ashis K / Fee, Timothy / Hilton, Benjamin / Layman, Lawrence / Hastie, Alex R / Chaubey, Alka / DuPont, Barbara R / Kolhe, Ravindra

The Journal of molecular diagnostics : JMD

2023 Volume 25, Issue 4, Page(s) 234–246

Abstract: The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic ... ...

Abstract	The standard-of-care diagnostic prenatal testing includes a combination of cytogenetic methods, such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA), using either direct or cultured amniocytes or chorionic villi sampling. However, each technology has its limitations: karyotyping has a low resolution (>5 Mb), FISH is targeted, and CMA does not detect balanced structural variations (SVs). These limitations necessitate the use of multiple tests, either simultaneously or sequentially, to reach a genetic diagnosis. Optical genome mapping (OGM) is an emerging technology that can detect several classes of SVs in a single assay, but it has not been evaluated in the prenatal setting. This validation study analyzed 114 samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity regions, 3 triploid genomes, 4 isochromosomes, and 1 translocation; and the method revealed the identity of 3 marker chromosomes and 1 chromosome with additional material not determined by karyotyping. In addition, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current standard-of-care methods for prenatal diagnostic testing.
MeSH term(s)	Pregnancy ; Female ; Humans ; In Situ Hybridization, Fluorescence ; Cytogenetic Analysis/methods ; Karyotyping ; Aneuploidy ; Chromosome Mapping ; Chromosome Aberrations ; Prenatal Diagnosis/methods ; Chromosome Disorders/diagnosis ; Chromosome Disorders/genetics
Language	English
Publishing date	2023-02-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2023.01.006
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Zs.A 5146: Show issues

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Article: Analytic Validation of Optical Genome Mapping in Hematological Malignancies.

Pang, Andy W C / Kosco, Karena / Sahajpal, Nikhil S / Sridhar, Arthi / Hauenstein, Jen / Clifford, Benjamin / Estabrook, Joey / Chitsazan, Alex D / Sahoo, Trilochan / Iqbal, Anwar / Kolhe, Ravindra / Raca, Gordana / Hastie, Alex R / Chaubey, Alka

Biomedicines

2023 Volume 11, Issue 12

Abstract: Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, ...

Abstract	Structural variations (SVs) play a key role in the pathogenicity of hematological malignancies. Standard-of-care (SOC) methods such as karyotyping and fluorescence in situ hybridization (FISH), which have been employed globally for the past three decades, have significant limitations in terms of resolution and the number of recurrent aberrations that can be simultaneously assessed, respectively. Next-generation sequencing (NGS)-based technologies are now widely used to detect clinically significant sequence variants but are limited in their ability to accurately detect SVs. Optical genome mapping (OGM) is an emerging technology enabling the genome-wide detection of all classes of SVs at a significantly higher resolution than karyotyping and FISH. OGM requires neither cultured cells nor amplification of DNA, addressing the limitations of culture and amplification biases. This study reports the clinical validation of OGM as a laboratory-developed test (LDT) according to stringent regulatory (CAP/CLIA) guidelines for genome-wide SV detection in different hematological malignancies. In total, 60 cases with hematological malignancies (of various subtypes), 18 controls, and 2 cancer cell lines were used for this study. Ultra-high-molecular-weight DNA was extracted from the samples, fluorescently labeled, and run on the Bionano Saphyr system. A total of 215 datasets, Inc.luding replicates, were generated, and analyzed successfully. Sample data were then analyzed using either disease-specific or pan-cancer-specific BED files to prioritize calls that are known to be diagnostically or prognostically relevant. Sensitivity, specificity, and reproducibility were 100%, 100%, and 96%, respectively. Following the validation, 14 cases and 10 controls were run and analyzed using OGM at three outside laboratories showing reproducibility of 96.4%. OGM found more clinically relevant SVs compared to SOC testing due to its ability to detect all classes of SVs at higher resolution. The results of this validation study demonstrate the superiority of OGM over traditional SOC methods for the detection of SVs for the accurate diagnosis of various hematological malignancies.
Language	English
Publishing date	2023-12-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720867-9
ISSN	2227-9059
ISSN	2227-9059
DOI	10.3390/biomedicines11123263
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Article ; Online: Genetic Predisposition to Neurological Complications in Patients with COVID-19.

Sahajpal, Nikhil Shri / Hastie, Alex R / Schieck, Maximilian / Mondal, Ashis K / Felde, Marc / van der Made, Caspar I / Chou, Janet S / Randolph, Adrienne G / Illig, Thomas / Zody, Michael C / Brownstein, Catherine A / Beggs, Alan H / Hoischen, Alexander / Chaubey, Alka / Kolhe, Ravindra

Biomolecules

2023 Volume 13, Issue 1

Abstract: Several studies have identified rare and common genetic variants associated with severe COVID-19, but no study has reported genetic determinants as predisposition factors for neurological complications. In this report, we identified rare/unique ... ...

Abstract	Several studies have identified rare and common genetic variants associated with severe COVID-19, but no study has reported genetic determinants as predisposition factors for neurological complications. In this report, we identified rare/unique structural variants (SVs) implicated in neurological functions in two individuals with neurological manifestations of COVID-19. This report highlights the possible genetic link to the neurological symptoms with COVID-19 and calls for a collective effort to study these cohorts for a possible genetic linkage.
MeSH term(s)	Humans ; COVID-19/complications ; COVID-19/genetics ; Genetic Predisposition to Disease ; Nervous System Diseases/genetics ; Genotype
Language	English
Publishing date	2023-01-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13010133
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