Topologically associating domain boundaries are required for normal genome function

Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and cause disease phenotypes1,2,3, but the overall extent to which this occurs remains unknown. Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal development. We used CRISPR genome editing in mice to individually delete eight TAD boundaries (11–80 kb in size) from the genome. All deletions examined resulted in detectable molecular or organismal phenotypes, which included altered chromatin interactions or gene expression, reduced viability, and anatomical phenotypes. We observed changes in local 3D chromatin architecture in 7 of 8 (88%) cases, including the merging of TADs and altered contact frequencies within TADs adjacent to the deleted boundary. For 5 of 8 (63%) loci examined, boundary deletions were associated with increased embryonic lethality or other developmental phenotypes. For example, a TAD boundary deletion near Smad3/Smad6 caused complete embryonic lethality, while a deletion near Tbx5/Lhx5 resulted in a severe lung malformation. Our findings demonstrate the importance of TAD boundary sequences for in vivo genome function and reinforce the critical need to carefully consider the potential pathogenicity of noncoding deletions affecting TAD boundaries in clinical genetics screening.This work was supported by U.S. National Institutes of Health (NIH) grants to L.A.P. and A.V. (UM1HG009421). Research was conducted at the E.O. Lawrence Berkeley National Laboratory and performed under U.S. Department of Energy Contract DE-AC02-05CH11231, University of California (UC). Phenotyping performed by the UC Davis Mouse Biology Program (MBP) (www.mousebiology.org) was funded by an NIH administrative supplement to the KOMP2 grant, 3UM1OD023221-07S1, for phenotyping non-coding elements. Adyam Akeza was supported by the NIH Bridges to Baccalaureate Program Grant R25GM095401 via UC Berkeley. J.L.-R. is supported by the Spanish Ministerio de Ciencia e Innovacion (PID2020-113497GB-I00).Peer reviewe

Single-cell, whole-embryo phenotyping of mammalian developmental disorders

Mouse models are a critical tool for studying human diseases, particularly developmental disorders. However, conventional approaches for phenotyping may fail to detect subtle defects throughout the developing mouse. Here we set out to establish single-cell RNA sequencing of the whole embryo as a scalable platform for the systematic phenotyping of mouse genetic models. We applied combinatorial indexing-based single-cell RNA sequencing to profile 101 embryos of 22 mutant and 4 wild-type genotypes at embryonic day 13.5, altogether profiling more than 1.6 million nuclei. The 22 mutants represent a range of anticipated phenotypic severities, from established multisystem disorders to deletions of individual regulatory regions. We developed and applied several analytical frameworks for detecting differences in composition and/or gene expression across 52 cell types or trajectories. Some mutants exhibit changes in dozens of trajectories whereas others exhibit changes in only a few cell types. We also identify differences between widely used wild-type strains, compare phenotyping of gain- versus loss-of-function mutants and characterize deletions of topological associating domain boundaries. Notably, some changes are shared among mutants, suggesting that developmental pleiotropy might be 'decomposable' through further scaling of this approach. Overall, our findings show how single-cell profiling of whole embryos can enable the systematic molecular and cellular phenotypic characterization of mouse mutants with unprecedented breadth and resolution

Magnitude And Leading Sites of Cancer in A Tertiary Cancer Care Hospital of Western Maharashtra

Context: It is observed that cancers are increasingly seen in both genders and all the age groups due to a complex interaction of various risk factors. To implement the public health intervention measures it is essential to have the baseline data regarding frequency, distribution of cancers in the population. Aims: To study the magnitude of cancers by obtaining a baseline data regarding the frequency, distribution, leading cancer sites among the patients in a tertiary cancer care hospital of Western Maharashtra. Study settings: Shri Siddhivinayak Ganapati Cancer Hospital, Miraj Study Design: Hospital based, Cross sectional study involving retrospective information of patients from 1st March 2005 to 28th February 2006. Methods and Material: Retrospective, questionnaire study of patients from 1st March 2005 to 28th February 2006. Out of the total 2168 new patients registered, 1891 patients were detected to be malignant and included in the study. Results: 63.5 % Males and 67% Females in the age group 35-64 years had cancer. The sex ratio percent was 1.01%. Top five Cancer in males in our study were Oral Cavity, Oesophagus, Lung, Larynx and NHL. Top five Cancer in females in our study were Cervix, Breast, Ovary, Oral Cavity and Oesophagus. 27% were TRCs (Tobacco Related Cancers) in males while 9.6% were TRCs in females. 34% cancers were in easily accessible parts of body. Conclusions: The Tobacco Related Cancers represent the most preventable form of cancer in our society. It was 27% in males and 9.6% in females in our study. Additionally, 34% cancers were in easily accessible parts of body. It highlights the possibility of easy and early detection of cancers in the population thus decreasing the cancer burden in the community

CLINICO-EPIDEMIOLOGICAL PROFILE OF ORAL CANCER: A HOSPITAL BASED STUDY

Background: India is heading towards various types of non-communicable diseases, which are also known as modern epidemics. Among these modern epidemics cancer is among the ten commonest cause of mortality in developing countries including India. Oral cancer is a major problem in India and accounts for 50-70% of all the cancers diagnosed. Ninety percent (90%) of oral cancers in South East Asia including India are linked to tobacco chewing and tobacco smoking. Research question: What is the profile of Oral cancer (Oral cavity) cases reported in the hospital? Objective: To study the clinico-epidemiological profile associated with Oral cancer cases. Methods: Study Design: Hospital based, Cross -sectional study. Settings: Shri Siddhivinayak Ganapati Cancer Hospital, Miraj, Maharashtra. Participants and Sample size: As it is a time bound study sample size comprised of all the confirmed cases of oral cancer reported in the hospital during the study period. The study was carried out from 1st March 2005 to 28th February 2006. Study variables included demographic factors, socioeconomic factors, enquiries regarding modifiable risk factors such as tobacco usage, alcohol consumption, site involved (within oral cavity), staging, histopathological examination, treatment modality used. Data entry and statistical analysis was done using Microsoft excel. Data presented in form of percentages and proportions. Results: Out of the total 160 cases, majority of the subjects were above 40 years age. 36 (22%) of subjects were young adults (below 40 years age). 125 (78%) subjects were male. Most of the subjects belonged to upper lower and lower middle socio-economic scale according to modified Kuppuswamy classification. It was observed that 139 (87%) cases consumed tobacco in all forms. Out of these, ninety cases consumed tobacco in chewable form. Tobacco was chewed mainly in the form of gutka. Only ten (10) female subjects chewed tobacco. No female subjects smoked. The most common site for oral cancer was tongue. Histopathologically 52 (32.5%) cases were well differentiated squamous cell carcinoma, 37 (23%) cases were moderately differentiated squamous cell carcinoma and 34 (21%) cases as poorly differentiated squamous cell carcinoma. 37 (23%) cases were diagnosed as Oral Verrucous Carcinoma (a rare variant of Oral Squamous Cell Carcinoma). 72% cases were in either stage II or stage III. Conclusions: The most common site for oral cancer was tongue and histopathologically majority of the cases were well differentiated squamous cell carcinoma presented in advanced stages of disease. We observed higher proportion of oral cancers among young patients (below 40 years). Proportion of Oral Verrucous Carcinoma (OVC) which is a rare variant of Oral Squamous Cell Carcinoma was also high in the study

A Study of Newly Detected Diabetes Mellitus Patients among Population of Rural Field Practice Area of a Tertiary Care Centre in Maharashtra

Background: Diabetes is traditionally known as silent disease and case detection require active and opportunistic screening efforts. Diabetes is no more restricted in urban areas only but is also estab- lished at rural areas as well. Material and methods: A cross sectional study was carried out in the field practice area of a tertiary care centre. A total of 290 par- ticipants who had given written informed consent were included in the study by camp approach. WHO guideline (2006) was used for diagnosis of diabetes. People showing fasting plasma glucose >126 mg/dl or 2 hour plasma glucose >200 mg/dl were diagnosed as diabetics. Results: Proportion of newly detected diabetes observed in the study was 7.5%. The newly detected diabetes cases increased i.e. 8 out of 143 (36.7%) in participants above age of 50 years as com- pared to 1 out of 38 (4.5%) in participants in age group 20-30 years. The proportion of diabetes was more in male participants i.e. 15 in 164 (8.4%) as compared to female participants i.e. 7 in 104 (6.3%). A significant association was found between diabetes and high BMI. Conclusion: The need for awareness regarding diabetes and its risk factors in the community is needed as many hidden cases were found. High BMI is one of the risk factor for diabetes melli- tus

Trends of Dengue Cases Reported at Tertiary Care Hospital of Metropolitan City of Maharashtra: A Record Based Study

Background & Objectives: Recent national data showed increasing trends of dengue prevalence but significant decrease in death rates.1Understanding trends and epidemiology of dengue outbreaks would help in effective control of dengue in city. Therefore, the research was planned to study & compare the trends of dengue cases reported at Tertiary hospital, state & district levels during 2009 to 2015. Methods: Six years data on ‘Dengue cases admitted in a tertiary care hospital’ was obtained from the Satellite Disease Surveillance Unit of Tertiary care hospital. District and state level data on dengue was mobilised from Public Health department authorities and websites. Tables and graphs were prepared. Data analysis and compilation was done with Microsoft Excel 2013. Result: A total of 56,981 patients with fever were screened for dengue at tertiary hospital during the study period. Of these, 5082 patients (8.91%) were tested positive. There was tenfold increase in the Dengue cases in six years. Rise of confirmed dengue cases was seen at District and state level. ‘Males’ and ‘Patients between 13-30 years age group’ were more affected. There was declining trend of dengue case fatality rate. Conclusion: Incresing trend of dengue indicates an alarming situation in the city and stressesmore preparedness during monsoon season

OCCUPATIONAL STRESS AND BURNOUTS AS PREDICTORS OF JOB SATISFACTION AMONGST LAWYERS IN DISTRICT SANGLI

Background: The practice of law is a high prestige, high skill, high income and high stress profession. The present study was conducted to find out the role of stressors on mental well being of the lawyers. Objectives: To study the occupational stress amongst the lawyers and to examine the correlates of job satisfaction in them, and to study the gender difference (if any) of stress and job satisfaction. Also to study the association between levels of stress and substance abuse disorders. Methodology: A cross sectional study was conducted in Dist. Court Sangli, which involved collection of data using predesigned proforma. By using Systematic Random sampling technique, out of total 240 lawyers 120(76 males and 44 females) were interviewed. Presumptive Stress Life Event Scale (PSLES) was used as a validated screening tool to calculate their Mental Stress Score. The level of Job Satisfaction was scored by 3 point scaling system taking 10 independent variables as the predictors of job satisfaction. Data was analyzed using appropriate statistical tests. Results: 88.3% lawyers had experienced stress. The female lawyers had high Mean Mental Stress Score. 81.8% female lawyers had high Job satisfaction Score i.e. low Job satisfaction. 52.8% of the male lawyers having stress reported substance abuse disorders. Conclusion: The female lawyers experience significantly greater stress and burnouts as compared to males. Job satisfaction is significantly and negatively correlated with stress. The need of the hour is to make an effort in coping with stress amongst lawyers