Publications

A cancer vaccine approach for personalized treatment of Lynch Syndrome

Snigdha Majumder, Rakshit Shah, Jisha Elias, Malini Manoharan, Priyanka Shah, Anjali Kumari, Papia Chakraborty, Vasumathi Kode, Yogesh Mistry, Karunakaran Coral, Bharti Mittal, Sakthivel Murugan SM, Lakshmi Mahadevan, Ravi Gupta, Amitabha Chaudhuri & Arati Khanna-Gupta.

Lynch Syndrome (LS) is an inherited heterozygous autosomal dominant disorder which predisposes affected individuals to the risk of developing colorectal cancer (CRC) as well as to endometrial carcinomas, tumours of the stomach, small intestines, ureter, brain, pelvis and prostate among others1. It is the most common hereditary CRC syndrome accounting for 2–5% of all CRCs. In the developed world, the estimated disease frequency ranges from 1:370 to 1:20002 but no prevalence details have been officially reported from developing nations to date. In India, while the overall incidence of CRC is comparatively lower than in the west, a large percentage of patients develop CRC before the age of 45 with a higher proportion (10–15%) of LS-CRC cases3.

https://www.nature.com/articles/s41598-018-30466-x
Becker’s Hospital Review: Tumor Microenvironment is a powerful companion diagnostic for cancer immunotherapy applications

Sam Santhosh, Hiranjith G.H., Michael Nemzek and Amitabha Chaudhuri.

Currently approved checkpoint inhibitors are antibodies that block the function of three key proteins expressed on the surface of T cells: CTLA-4, PD-1 and PD-L1. Under normal conditions, these proteins function as brakes to prevent immune-related toxicity from arising because of persistent T cell activity. Cancer hijacks this essential function of immune homeostasis to protect itself from immune- mediated elimination [1, 2]. By expressing high levels of PD- L1, tumor cells engage PD-1 receptors on T cells, suppressing their anti-tumor activity and escaping T cell-mediated killing. By blocking PD-1 and PD-L1 signaling, the checkpoint inhibitors remove the brakes on T cells imposed by the tumor and enhance their anti-tumor activity

https://www.medgenome.com/pdf/publications/MedgenomeReprint.pdf
Tumor Microenvironment is a powerful companion diagnostic for cancer immunotherapy applications

Sam Santhosh, Hiranjith G.H., Michael Nemzek and Amitabha Chaudhuri.

Currently approved checkpoint inhibitors are antibodies that block the function of three key proteins expressed on the surface of T cells: CTLA-4, PD-1 and PD-L1.

Under normal conditions, these proteins function as brakes to prevent immune-related toxicity from arising because of persistent T cell activity. Cancer hijacks this essential function of immune homeostasis to protect itself from immune-mediated elimination [1, 2]. By expressing high levels of PD-L1, tumor cells engage PD-1 receptors on T cells, suppressing their anti-tumor activity and escaping T cell-mediated killing. By blocking PD-1 and PD-L1 signaling, the checkpoint inhibitors remove the brakes on T cells imposed by the tumor and enhance their anti-tumor activity [3].

https://www.beckershospitalreview.com/quality/tumor-microenvironment-is-a-powerful-companion-diagnostic-for-cancer-immunotherapy-applications.html
Ancient human migrations to and through Jammu Kashmir- India were not of males exclusively

Indu Sharma, Varun Sharma, Akbar Khan, Parvinder Kumar, Ekta Rai, Rameshwar N. K. Bamezai, Miguel Vilar & Swarkar Sharma.

Jammu and Kashmir (J&K), the Northern most State of India, has been under-represented or altogether absent in most of the phylogenetic studies carried out in literature, despite its strategic location in the Himalayan region. Nonetheless, this region may have acted as a corridor to various migrations to and from mainland India, Eurasia or northeast Asia. The belief goes that most of the migrations post-late Pleistocene were mainly male dominated, primarily associated with population invasions, where female migration may thus have been limited. To evaluate female-centered migration patterns in the region, we sequenced 83 complete mitochondrial genomes of unrelated individuals belonging to different ethnic groups from the state. We observed a high diversity in the studied maternal lineages, identifying 19 new maternal sub-haplogroups (HGs). High maternal diversity and our phylogenetic analyses suggest that the migrations post-Pleistocene were not strictly paternal, as described in the literature. These preliminary observations highlight the need to carry out an extensive study of the endogamous populations of the region to unravel many facts and find links in the peopling of India.

https://www.nature.com/articles/s41598-017-18893-8?error=cookies_not_supported&code=69e3d22c-ec23-4bd1-8fb6 2b8f909ac04c
Next-generation sequencing reveals novel mutations in X-linked intellectual disability

Muthusamy B, Selvan LDN, Nguyen TT, Manoj J, Stawiski EW, Jaiswal BS, Wang W, Raja R, Ramprasad VL, Gupta R, Murugan S, Kadandale JS, Prasad TSK, Reddy K, Peterson A, Pandey A, Seshagiri S, Girimaji SC, Gowda H, OMICS, 2017 May;21(5):295-303.

Robust diagnostics for many human genetic disorders are much needed in the pursuit of global personalized medicine. Next- generation sequencing now offers new promise for biomarker and diagnostic discovery, in developed as well as resource-limited countries. In this broader global health context, X-linked intellectual disability (XLID) is an inherited genetic disorder that is associated with a range of phenotypes impacting societies in both developed and developing countries. Although intellectual disability arises due to diverse causes, a substantial proportion is caused by genomic alterations. Studies have identified causal XLID genomic alterations in more than 100 protein-coding genes located on the X-chromosome. However, the causes for a substantial number of intellectual disability and associated phenotypes still remain unknown. Identification of causative genes and novel mutations will help in early diagnosis as well as genetic counseling of families. Advent of next-generation sequencing methods has accelerated the discovery of new genes involved in mental health disorders. In this study, we analyzed the exomes of three families from India with nonsyndromic XLID comprising seven affected individuals. The affected individuals had varying degrees of intellectual disability, microcephaly, and delayed motor and language milestones. We identified potential causal variants in three XLID genes, including PAK3 (V294M), CASK (complex structural variant), and MECP2 (P354T). Our findings reported in this study extend the spectrum of mutations and phenotypes associated with XLID, and calls for further studies of intellectual disability and mental health disorders with use of next-generation sequencing technologies.

https://www.ncbi.nlm.nih.gov/pubmed/28481730
The utility and futility of targeted Next-generation sequencing for carrier detection in 'At Risk' couples

Sunita Bijarnia-Mahay, Deepti Gupta, V L Ramprasad, Sakthivel Murugan, Renu Saxena, Sudha Kohli, Seiji Yamaguchi, Yosuke Shigematsu and I C Verma, Genetic Clinics 2017, January – March, Vol 10, Issue 1.

Next generation sequencing has changed the approach to genetic diagnosis and testing in recent times. The days have arrived when a molecular genetic diagnosis can be attempted even without the availability of the proband or affected person. However this requires additional strong evidence of diagnosis in the proband, such as biochemical or radiological hallmarks. Needless to say, this attempt should always be made during counseling to make the family aware of the fallacies and limitation involved due to non-availability of the sample of the proband. Since many recessive disorders are either fatal or severely debilitating and burdensome, with no easy treatment, the NGS technology has provided a much needed relief in terms of testing and prevention in family by enabling prenatal diagnosis, at least in a few cases. Encouraging results have been shown upon testing of the proband directly. However, the final word remains to be said on complete reliability of the method for carrier testing, performed without availability of the proband. We present two similar cases, of methyl malonic acidemia, where use of NGS resulted in contrasting outcomes after genetic testing for carrier status, thus highlighting the utility and the futility of the test in certain situations. While a correct identification of mutations in the first couple (in the MMAB gene) resulted in successful prenatal diagnosis and prevention of recurrence, an inability to identify the disease and mutation resulted in birth of an affected baby with MMA in the second family.

http://iamg.in/genetic_clinics/adm/articlepdf/genevista_January_March_2017.pdf
Manitoba Oculotrichoanal Syndrome: First case report from India

Sai Rani Karanam, Vinay Kumar Konana, Shruthi Sreenivasaiah, Sudhakar Potti, Delhi Journal of Ophthalmology (2016).

Manitoba-oculo-tricho-anal (MOTA) syndrome is very rare syndrome characterized by aberrant hairline, eye anomalies (ocular hypertelorism, cryptophthalmos, and upper eyelid colobomas), bifid nose, omphalocele and anorectal anomalies. MOTA syndrome was first reported in 1992 in Oji-cree community from the Island Lake region of Manitoba, Canada. Till date very few cases of MOTA have been reported and none from India. We report first case of MOTA syndrome from India. A two month old male baby was brought with complaints of defect in right upper eye lid since birth. He was the second born child of a second degree consanguineously married couple at 37 weeks of gestation. On physical examination, the baby had right upper eyelid coloboma, ocular hypertelorism, bifid nose, small nasal ala and bilateral undescended testis. Investigations revealed high anorectal anomaly and right renal agenesis. Whole exome sequencing showed homozygous nonsense variation in exon 25 of the FREM1 gene that resulted in a stop codon. This case gains importance as it is the first case of MOTA being reported from India and bilateral undescended testis which was seen this case is an addition to the variable clinical spectrum of MOTA.

http://www.djo.org.in/articles/27/2/manitoba-oculotrichoanal.html
A splice site mutation in HERC1 leads to Syndromic Intellectual Disability with macrocephaly and facial dysmorphism: Further delineation of the phenotypic spectrum

Aggarwal S, Bhowmik AD, Ramprasad VL, Murugan S, Dalal A, Am J Med Genet A. 2016 Jul;170(7):1868-73.

We report on a sib pair of Indian origin presenting with intellectual disability, dysmorphism, and macrocephaly. Exome sequencing revealed a homozygous splice site HERC1 mutation in both probands. Functional analysis revealed use of an alternate splice site resulting in formation of a downstream stop codon and nonsense mediated decay. In the light of recent reports of HERC1 mutations in two families with a similar phenotypic presentation, this report reiterates the pathogenic nature and clinical consequences of HERC1 disruption.

https://www.ncbi.nlm.nih.gov/pubmed/27108999
Sequencing and analysis of a South Asian-Indian personal genome

Ravi Gupta, Aakrosh Ratan, Changanamkandath Rajesh, Rong Chen, Hie Lim Kim, Richard Burhans, Webb Miller, Sam Santhosh, Ramana V Davuluri, Atul J Butte, Stephan C Schuster, Somasekar Seshagiri and George Thomas (2012). BMC Genomics, 13, 440.

With over 1.3 billion people, India is estimated to contain three times more genetic diversity than Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala.

https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-440
Recessive mutations in SLC38A8 cause Foveal Hypoplasia and Optic Nerve Misrouting without Albinism

James A. Poulter, Musallam Al-Araimi, Ivan Conte, Maria M. van Genderen, Eamonn Sheridan, Ian M. Carr, David A. Parry, Mike Shires, Sabrina Carrella, John Bradbury, Kamron Khan, Phillis Lakeman, Panagiotis I. Sergouniotis, Andrew R. Webster, Anthony T. Moore, Bishwanath Pal, Moin D. Mohamed, Anandula Venkataramana, Vedam Ramprasad, Rohit Shetty, Murugan Saktivel, Govindasamy Kumaramanickavel, Alex Tan, David A. Mackey, Alex W. Hewitt, Sandro Banfi, Manir Ali, Chris F. Inglehearn, and Carmel Toomes (2013). The American Journal of Human Genetics, 93, 1143–1150.

Foveal hypoplasia and optic nerve misrouting are developmental defects of the visual pathway and only co-occur in connection with albinism; to date, they have only been associated with defects in the melanin-biosynthesis pathway. Here, we report that these defects can occur independently of albinism in people with recessive mutations in the putative glutamine transporter gene SLC38A8. Nine different mutations were identified in seven Asian and European families. Using morpholino-mediated ablation of Slc38a8 in medaka fish, we confirmed that pigmentation is unaffected by loss of SLC38A8. Furthermore, by undertaking an association study with SNPs at the SLC38A8 locus, we showed that common variants within this gene modestly affect foveal thickness in the general population. This study reveals a melanin-independent component underpinning the development of the visual pathway that requires a functional role for SLC38A8.