Molecular and Genetic Medicine

Background: Human Papillomavirus and cervical cancer have become a major preoccupation for the medical and scientific international communities. Human Papillomavirus leads to precancerous lesions that can evolve in cervical cancer. Senegal is ranked 15^th in the world for the incidence of cervical cancer. According to WHO, cervical cancer represented 30% of all deaths by cancer among women, representing the most frequent death by cancer in Senegal, followed by breast cancer (15.5%). The most frequent types of HPV found in cervical cancer are 16, 18, 31, 33, 35, 45, 52 and 58.

Objectives: The objective of our study is to evaluate, using molecular methods, the prevalence of HPV among Senegalese women and identify risk factors.

Materials and Methods: A total of 142 cervicals samples were collected from Senegalese women. The endocervix samples were used for identifying 14 types of HPV-HR of which (16 and 18 specified by their genotype) and (31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68 not specified) using Abbott m2000sp/m2000rt RealTime High Risk HPV.

Results: The prevalence of HPV-HR was 12.7%. The 12 types of not specified HPV-HR showed a prevalence of 10.6%. Types 16 and 18 were identified in a respective proportion of 1.4% and 0.7%, no co-infection was identified. The risk of developing HPV-HR infection is independently associated (P ˃ 0.05) with the aspect of the cervix, age, ethnics groups, contraception, and the age first sexual intercourse. However, HPV-HR infection prevalence is significantly higher (P˂0.05) in women that are single/widowed/divorced (41.7%), who went through multiples miscarriage (14.3%), with multiples sexual partner (16.4%), active smoking and alcohol consumption (40%).

Conclusion: These results highlight the need for a new preventive vaccine against all HPV-HR. The value of monitoring risk factors for impactful public health address is critical for the screening of HPV-HR in sub-Saharan women.

Neuroendocrine tumors (NET) are a mysterious group of malignancies that can form throughout the diffuse neuroendocrine system and produce biological effects distant from their primary location. They have an increasing incidence and can also behave more aggressively than previously recognized. These heterogeneous features have interfered with a more fundamental understanding of tumor biology. Over the past several years, systematic genetic surveys NETs from the major sites of origin have revealed important genomic changes, with potential driver mutations, that have an impact on prognosis and clinical development of targeted therapies. We will take a focused approach in reviewing this data and its impact on clinical medicine.

Genome-scale metabolic models (GSMMs) have been widely used to study the molecular mechanisms underlying a variety of diseases with a strong metabolic component such as diabetes or cancer. GSMMs incorporate logical rules associating genes, proteins, and reactions (GPR rules), enabling the integration of either proteomics or transcriptomics. However, current GPR formulation do not account for the necessary stoichiometry to describe the number of transcript copies that are necessary to generate a catalytically active enzyme, which limits our understanding of how gene expression modulates metabolism. Thus, in this short commentary article, we introduce the stoichimetric-GPR (S-GPR) concept, presented in Marin de Mas I et al. The novel S-GPRs associations were implemented to study the metabolic reprogramming in DU145 prostate cancer cells associated to the chronic exposure to the endocrine disruptor Aldrin. The results showed that S-GPRs outperformed previous approaches by significantly improving the GSMM predictions. Thus, the novel S-GPR concept that we have developed enables a more precise integration of transcriptomics data into GSMM-based methods and can be extended to proteomics data, with an important impact in the environmental and the clinical fields.

Duchenne Muscular Dystrophy (DMD) is a X linked genetic disorder that causes difficulty in walking, followed by progressive skeletal muscle degeneration and some cardiac muscle related issues, that threatens the life expectancy of patients. This condition is due a mutation in a gene that produces cytoskeletal protein termed as dystrophin. Targeting this gene to correct or bypass the mutation would benefit in effective therapies for DMD. CRISPR/Cas9 (Clustered Regularly Interspaced Palindromic Repeats) technology has created an evolution in precise gene modification techniques. With the help of a guide RNA, Cas9 (a DNA endonuclease) can create a double strand breaks to carry out the targeted gene modifications. By simply modifying the guide RNA sequences, Cas9 can be used for flexible programming of new target sites. The prime factor that determines the therapeutic efficiency of gene editing is the delivery vector. Lot of attempts has been made to create an efficient therapy for DMD with CRISPR/Cas9, but still, the major hurdles rely on delivery techniques. Therefore, optimization of the delivery methods will support the complete regenerative therapy for DMD in future. This review mainly concentrates on the various aspects of CRISPR/Cas9 technologies and its delivery methods used in developing therapies for DMD and its optimization possibilities.

Estrogen receptor alpha (ESR1) plays an important role in many tissues including the liver. Numerous alternative splice variants of ESR1 exist that encode ESR1 proteins with varying functions. We aim to study ESR1 genomic organization and its mRNA expression profile in human liver by incorporating information from literature and genomic databases (Ensembl, NCBI and GTEx), and employing a quantitative method to measure all known ESR1 mRNA splice variants in 36 human livers. We re-constructed ESR1 genomic organization map that contains 29 exons. ESR1 mRNA splice variants with varying 5’ untranslated region (5’UTR) and/or missing each of eight coding exons are readily detectable in liver and other tissues. Moreover, we found extensive inter-individual variability in splice variant pattern of ESR1 transcripts. Specifically, ESR1 transcripts lacking first coding exon are the main transcripts in liver, which encode ESR1 proteins missing N-terminal 173 amino acids (for example, ERα46), reported previously to have either constitutive activity or dominant negative effects depending on cellular context. Moreover, some livers predominantly express ESR1 transcripts missing exon 10 or 16, encoding C-terminal truncated ESR1 proteins with varying ESR1 activities. Inter-person variability in ESR1 expression profile may contribute to inter-person variability in drug metabolism and susceptibility to liver related diseases.

Aim: To understand the genetic disease spectrum in a hospital setting using exome analysis by NGS technology.

Methods: We have applied clinical exome studies in our patient groups who presented for a year from 1^st April 2017 to 31^st March 2018. The data were from all patients from the hospital records irrespective of age and sex from any background who were either referred to or had a direct OPD walk in to the genetic clinic. Those patients who had a suspected family history of a genetic disease were included for testing. The test was applied only in cases if there was a definitive phenotypic evidence of the condition. The patients were included irrespective of a specialty of referral.

Results: Among a total of 171 families who sought clinical consultation, exome analysis were indicated in 33 patients. In that, 25 patients had a molecular positivity for the suspected condition and 8 members had been ruled out of the disease. Genetic counselling was given to all 171 patients and in many cases; an extended family screening and counselling were given. The genotype-based prognostication was added to the phenotype prognostication in these patients for the first-time adding value to the patient care not only in diagnosis but also in making management decisions incorporating the new knowledge.

Conclusion: This study is now our basic framework for genotype-based follow-up in our patient groups and an impetus to practice clinical genomic medicine at a hospital level. This is the first time we have incorporated diagnostic sequencing in South India at a hospital setting.

Aim: Autism Spectrum Disorder (ASD) is a prevalent neuropsychiatric condition affecting a person’s ability to interact and socialize. It varies in severity, but the majority are unable to work or develop partnerships. There are currently no treatments. Microflora abnormalities have been investigated in relation to the neuropsychiatric manifestations in ASD. Various abnormalities have been identified, and to date there are no refutation studies discoverable.

Methods: A total of 147 patients with ASD had undergone quantitative Polymerase Chain Reaction (qPCR) stool analysis at initial presentation and had been free from antibiotics for the previous three months. The proportion of firmicutes to bacteriodetes phyla were calculated in a percentage ratio. Controls were taken from patients who had attended the outpatient clinic around the same time, had not had antibiotics for three months and did not have a diagnosis of ASD.

Results: There was a significant increase in the proportion of firmicutes in the patients with ASD versus controls (63:37 in ASD patients (n=147) versus 55:45 in controls (n=12), mean difference of 8.6% P=0.005, CI=3.1 – 12.9). Significance remained after correction for age and sex.

Conclusion: In this retrospective analysis, patients with ASD had a significantly different composition of microflora than unhealthy controls. This adds to the growing body of evidence that ASD patients have abnormal microflora. Longitudinal population studies examining a potential causal link between microflora and ASD onset/ symptomology are crucial for examining preventative, harm-reduction and treatment interventions in this oftendebilitating condition.