Novel oncogenic transcriptional targets of mutant p53 in esophageal squamous cell carcinoma

Missense mutations in the DNA binding domain of p53 are observed frequently in esophageal squamous cell carcinoma (ESCC). Recent studies have revealed the potentially oncogenic transcriptional networks regulated by mutant p53 proteins. However, majority of these studies have focused on common "hotspot" p53 mutations while rarer mutations are poorly characterized. In this study, we report the characterization of rare, "non-hotspot" p53 mutations from ESCC. In vitro tumorigenic assays performed following ectopic-expression of certain "non-hotspot" mutant p53 proteins caused enhancement of oncogenic properties in squamous carcinoma cell lines. Genome-wide transcript profiling of ESCC tumor samples stratified for p53 status, revealed several genes exhibiting elevated transcript levels in tumors harboring mutant p53. Of these, ARF6, C1QBP, and TRIM23 were studied further. Reverse transcription-quantitative PCR (RT-qPCR) performed on RNA isolated from ESCC tumors revealed significant correlation of TP53 transcript levels with those of the three target genes. Ectopic expression of wild-type and several mutant p53 forms followed by RT-qPCR, chromatin affinity-purification (ChAP), and promoter-luciferase assays indicated the exclusive recruitment of p53 mutants-P190T and P278L, to the target genes leading to the activation of expression. Several functional assays following knockdown of the target genes revealed a significant suppression of tumorigenicity in squamous carcinoma cell lines. Rescue experiments confirmed the specificity of the knockdown. The tumorigenic effects of the genes were confirmed in nude mice xenograft assays. This study has therefore identified novel oncogenic targets of "non-hotspot" mutant p53 proteins relevant for ESCC besides validating the functional heterogeneity of the spectrum of tumor-specific p53 mutations.

Abstract 2494: Identification of novel oncogenic targets of mutant p53 in esophageal squamous cell carcinoma

Background: Mutations in the TP53 gene are observed at a high frequency in Esophageal Squamous Cell Carcinoma (ESCC) with a majority of alterations being of the missense type affecting residues located in the region encoding the DNA binding domain. These mutations are associated with poor patient survival. However, characterization of the transcriptional networks regulated by p53 mutant proteins is limited to only a few frequent ‘hotspot' mutants, while comparatively rarer mutants have not been characterized.

Objectives: Identification and characterization of differentially expressed genes associated with p53 mutation status in ESCC tumor samples. Elucidation of the mechanism of transcriptional regulation of mutant p53 target genes.

Methods: A defined set of ESCC tumor samples with known p53 mutation status was selected for this study. The ability of each 'rare' p53 mutation to modulate tumor-related phenotypes was evaluated by performing phenotypic assays such as proliferation, colony formation and migration, in head and neck cancer cell-lines. Gene expression microarray analysis was performed on 36 ESCC tumors to determine putative target genes of 'rare' p53 mutant forms. Following dimension reduction, differentially expressed (putative mutant p53 target) genes were identified using Significance Analysis of Microarrays (SAM) and validated using reverse transcription quantitative PCR (RT-qPCR). Transcription induction of the putative target genes by ectopically expressed wild-type and mutant p53, in p53-null H1299 cell-line, were also evaluated by RT-qPCR. Chromatin immuno-precipitation (ChIP) assay was used to determine localization of mutant p53 proteins to chromosomal loci harboring the putative target genes. Similarly, ability to activate target promoters by mutant p53 was validated through promoter-luciferase assay.

Results: Genome-wide analysis revealed 27 differentially expressed genes, of which 9 exhibited up-regulated transcript levels in p53 mutant tumors. Three putative mutant p53 target genes - C1QBP, ARF6 and TRIM23 - were selected for further analysis due to previous reports of their association with cancer. TP53 transcript levels positively correlated with transcript levels of the identified potential mutant targets. The ectopically-expressed p53 mutants - P190T and P278L, induced the increased expression of the target genes, were localized to and activated the promoters of the target genes. Further characterization of the target genes is currently underway.

Conclusions: Three novel potential oncogenic targets of mutant p53 proteins were identified. The study further strengthened the heterogeneity in the functioning of different p53 mutants.

Citation Format: Sara A. George, Viswakalyan Kotapalli, Raju S. Adduri, Raju Kumar, Sanjana Sarkar, Ramaswamy Pandilla, Murali D. Bashyam. Identification of novel oncogenic targets of mutant p53 in esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2494.

Multiple oncogenic roles of nuclear beta-catenin

β-Catenin is essential for embryonic development and required for cell renewal/regeneration in adult life. Cellular β-catenin exists in three different pools: membranous, cytoplasmic and nuclear. In this review, we focus on functions of the nuclear pool in relation to tumorigenesis. In the nucleus, beta-catenin functions as both activator and repressor of transcription in a context-dependent manner. It promotes cell proliferation and supports tumour growth by enhancing angiogenesis. β-Catenin-mediated signalling regulates cancer cell metabolism and is associated with tumour-initiating cells in multiple malignancies. In addition, it functions as both pro- and anti-apoptotic factor besides acting to inhibit recruitment of inflammatory anti-tumour T-cells. Thus, β-catenin appears to possess a multifaceted nuclear function that may significantly impact tumour initiation and progression.

Abstract 2500: Identification and characterization of a bipartite nuclear localization signal reveals non-canonical 'oncogenic' role for cytoplasm-restricted ARID1B

The AT-rich interaction domain-containing protein 1B (ARID1B/ BAF250b) is a component of SWItch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex that functions as the primary chromatin remodeler during ontogeny and adult life. ARID1B is classified as a tumor suppressor in melanoma as well as in cancers of the uterus, ovary, lung, breast, colon and pancreas. Though human ARID1B is a nuclear protein, the molecular basis of its nuclear import is not understood. Using protein truncation analysis, in silico prediction and sequence comparison within forty three metazoan species, we identified a putative bipartite Nuclear localization signal (NLS) sequence, further confirmed by immunofluorescence analyses and cell fractionation followed by immunoblotting. An immunoprecipitation-mass spectrometry based screen for identifying ARID1B interacting proteins revealed members of the importin family (IPO5, KPNA2 and KPNB1). In addition, ARID1B nuclear import was inhibited by Importazole (general importin β inhibitor). Transcription activation function of the cytoplasm-restricted ARID1B-NLS mutant, as measured by quantifying CDKN1A and CDKN1B transcript and protein levels as well as promoter activity following ectopic expression in cancer cell lines, was significantly compromised when compared to wild type ARID1B. The NLS-mutant was also restricted in its ability to induce senescence. Surprisingly however, cytoplasmic localization of ARID1B appeared to result in an ‘oncogenic' gain of function as it boosted cell proliferation, promoted ERK signaling and activated β-catenin/TCF-LEF function. A detailed analysis of the oncogenic role of cytoplasm-restricted ARID1B is ongoing. A careful scrutiny of various cancer specific somatic mutation databases revealed several mutations located within the ARID1B NLS sequence. In addition, ARID1B immunohistochemistry on breast cancer tissue microarrays (TMAs) revealed significant cytoplasmic localization. These observations suggest possible clinical relevance of cytoplasm-restricted ARID1B. Functional validation of NLS specific mutations and TMA analysis of other cancers is currently underway. Non-canonical oncogenic gain of function due to aberrant cytoplasmic localization has been shown previously for classical tumor suppressors such as pRB, p27, p21 and p53. Our results have revealed a novel ‘oncogenic' facet of ARID1B resulting from its aberrant cytoplasmic localization.

Citation Format: Srinivas Animireddy, Padmavathi Kavadipula, Viswakalyan Kotapalli, Swarnalata Gowrishankar, Satish Rao, Murali D. Bashyam. Identification and characterization of a bipartite nuclear localization signal reveals non-canonical 'oncogenic' role for cytoplasm-restricted ARID1B [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2500.

Abstract 3692: Transcriptome analysis of oral tongue cancer reveals novel insights into wild type and mutant TP53 transcription program

The p53 oncoprotein is a tumor suppressor that is stabilized upon various forms of cellular stresses to induce transcription of genes regulating cell cycle arrest or apoptosis. TP53 is the most frequently mutated gene in human cancers and majority of mutations are located in the region encoding the DNA binding domain compromising thereby its transcription activation ability and resulting in loss of function. Recent studies however suggest mutant p53 proteins to exhibit a gain of function property. Specific p53 missense mutations can result in an altered transcription program causing positive regulation of cell proliferation, metastasis and chemoresistance. In our previous studies, we performed comprehensive characterization of squamous cell carcinoma of the oral tongue (SCCOT) with respect to p53, EGFR, Wnt, MSI, LoH of several tumor suppressor loci and HPV status. Mutant p53 was a significant predictor of overall survival and the TP53 codon 72 Proline allele was significantly associated with SCCOT. In order to dissect the role of mutant p53 in tongue cancer, we performed genome wide DNA and RNA profiling of 26 and 40 SCCOT samples, respectively. Both mutant and wild type tumor samples appeared to exhibit comparable levels of DNA copy number alterations. Transcriptome data analyses using a combination of single sample gene set enrichment analysis and comparative marker selection revealed gene sets that could significantly distinguish p53 mutant and wild type tumor samples. Significance analysis of microarrays performed on all genes constituting the differentially enriched gene sets surprisingly identified only two genes to be upregulated in p53 mutant samples at a false discovery rate significantly lower than 10% namely TP53 itself and SMARCD1; the latter a member of the SWI/SNF chromatin remodelling complex. Elevated levels of TP53 transcript in tumors harbouring mutant p53 significantly correlated with levels of ZMAT3, itself induced by p53 and known to stabilize the TP53 transcript. In addition, the analysis revealed several known (ATF3 and others) and novel (GCHFR and others) targets of wild type p53. Differential expression of all targets was validated in additional tongue cancer samples. Ectopic expression of certain (but not all) p53 mutant proteins in p53 null cells induced SMARCD1 (but not canonical wild type p53 targets) while expression of wild type p53 induced GCHFR, ATF3, CDKN1A, etc. (but not SMARCD1). In contrast, p53 stabilization in cells harboring wild type p53 caused elevation of GCHFR, ATF3, CDKN1A, etc., but not of SMARCD1. Validation of novel targets using promoter-luciferase constructs, chromatin immunoprecipitation PCR and a tongue cancer tissue microarray is underway. This is perhaps the first evidence from Head and Neck tumor samples for a gain of function activity of mutant p53. Thus wild type and mutant p53 may support distinct transcription programs in tongue cancer.

Citation Format: Raju SR Adduri, Padmavathi Kavadipula, Viswakalyan Kotapalli, Leena Bashyam, Anupama Shirke, Arun kumar Paripati, Swarnalata Gowrishankar, Mukta Srinivasulu, Mohammed Mujtaba Ali, Subramanyeshwar Rao, Snehalatha Dhagam, Mohana Vamsy Chigurupati, Shantveer G. Uppin, Vijaya Tourani, Murali D. Bashyam. Transcriptome analysis of oral tongue cancer reveals novel insights into wild type and mutant TP53 transcription program. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3692.

Fucoidan from Turbinaria conoides: a multifaceted 'deliverable' to combat pancreatic cancer progression

The presence of occult metastases at the time of diagnosis together with the lack of effective chemotherapies pose a dire need for designing new and targeted therapeutics for pancreatic cancer. Fucoidans from brown algae can be regarded as potential candidates in view of their antioxidant, anti-cancer and anti-angiogenic potential. Herein, we investigated the antioxidant and anti-cancer effects of fucoidans, sulfated polysaccharides from Turbinaria conoides (TCFE) in pancreatic cancer cell lines. TCFE exerted significant antioxidant activities against various free radicals. Significant inhibition of cell proliferation and, induction of apoptotic cell death were observed in pancreatic cancer cells in response to TCFE. Also, TCFE exhibited significant anti-angiogenic potential. Evidently, gelatin zymography revealed that TCFE inhibited matrix metalloproteases -2 and -9 activities in pancreatic cancer cells. These results clearly indicate that TCFE could serve as a potential 'deliverable' to alleviate pancreatic cancer progression by inhibiting tumor cell proliferation and angiogenesis.

Evidence for presence of mismatch repair gene expression positive Lynch syndrome cases in India

Lynch syndrome (LS), the most common form of familial CRC predisposition that causes tumor onset at a young age, is characterized by the presence of microsatellite instability (MSI) in tumors due to germline inactivation of mismatch repair (MMR) system. Two MMR genes namely MLH1 and MSH2 account for majority of LS cases while MSH6 and PMS2 may account for a minor proportion. In order to identify MMR genes causing LS in India, we analyzed MSI and determined expression status of the four MMR genes in forty eight suspected LS patient colorectal tumor samples. Though a majority exhibited MSI, only 58% exhibited loss of MMR expression, a significantly low proportion compared to reports from other populations. PCR-DNA sequencing and MLPA-based mutation and exonic deletion/duplication screening respectively, revealed genetic lesions in samples with and without MMR gene expression. Interestingly, tumor samples with and without MMR expression exhibited significant differences with respect to histological (mucin content) and molecular (instability exhibited by mononucleotide microsatellites) features. The study has revealed for the first time a significant proportion of LS tumors not exhibiting loss of MMR expression.

Abstract 1883: Clinical and molecular genetic analysis of squamous cell carcinoma of the oral tongue

Squamous cell carcinoma of tongue (SCCT) is a common form of head and neck squamous cell carcinoma (HNSCC) in developing countries, mainly in India. In the last few decades, a steady increase in incidence rate of SCCT has been reported across the world. More importantly, though SCCT is considered to be a tobacco-related late-onset cancer, recent reports indicate an increase in incidence of SCCT in the young and in non-smokers. We analyzed the status of known tumorigenic pathways/genes including TP53, epidermal growth factor receptor (EGFR), microsatellite instability (MSI), CDKN2A, FHIT and human papilloma virus (HPV) infection in 120 surgically resected primary oral SCCT (SCCOT) samples and correlated with clinico-pathological variables and disease specific survival. 78 of 121 (65%) samples exhibited p53 nuclear stabilization confirming earlier reports. Interestingly, p53 nuclear stabilization was more common in young (36/46; 78%) than in older (44/75; 56%) patients (p = 0.0184). Further, PCR based mutation screening of exons 5-8 (encoding the DNA binding domain of p53) revealed mutations in ten of nineteen samples (52.6%) that exhibited p53 nuclear stabilization and in three of fifteen tumors (20%) that did not. We identified a novel 33bp deletion, c.616-648del33, located in exon 5 in a p53 positive tumor from a chronic tobacco chewer. Case control analysis revealed that Proline at TP53 codon 72 increased the risk of SCCOT. Majority of samples (97/121; 80%) exhibited significant EGFR expression though HPV infection was rare (14/106; 13%). MSI was observed in 14/106 (13%) samples, a frequency higher than reported for other populations. Loss of Heterozygosity (LOH) was more frequently observed in CDKN2A (28%) and FHIT (26%). In addition, LOH at FHIT locus was significantly associated with p53 nuclear stabilization (p = 0.0508), especially in non-smokers. A significant difference in survival rate between p53 positive and negative group (p = 0.0056) (Hazard ratio 2.5595) was observed. Though associated with p53 stabilization, FHIT loss did not exhibit significant effect on patient survival. Interestingly, patients exhibiting p53 nuclear stabilization as well as FHIT loss exhibited worse survival. We performed genome-wide DNA copy number and transcript profiling in several SCCOT samples. Interestingly, there was no significant difference in extent and profile of chromosomal instability in p53 positive and negative tumors. Amplifications were detected at chromosomal regions 3q26.1 (PIK3CA), 5p, 8q22 (MYC, RUNX1T1), 11q13 (CCND1) and 20q13 (HNFα). Genome-wide transcript profiling identified novel pathways that appear to drive tumorigenesis in tumors not exhibiting p53 inactivation. Our comprehensive analysis has therefore revealed important insights into the molecular basis for SCCOT and identified prognostic indicators in patients not associated with tobacco use.

Citation Format: Raju S. Adduri, Viswakalyan Kotapalli, Rajender K K, Swarnalata Gowrishankar, Saumyadipta Pyne, Mukta Srinivasulu, Subramanyeshwar Rao, Shantveer G. Uppin, Mohammed Mujtaba Ali, Umanath K. Nayak, Snehalatha Dhagam, Mohana Vamsy Chigurupati, Murali D. Bashyam. Clinical and molecular genetic analysis of squamous cell carcinoma of the oral tongue. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1883. doi:10.1158/1538-7445.AM2014-1883

Abstract 1285: Identification of MMR gene exonic rearrangements in suspected Lynch syndrome tumors without loss of MMR expression

Lynch syndrome (LS), also called Hereditary Non-Polyposis Colorectal Cancer, the most well studied form of familial CRC, is responsible for about 3% of all CRC cases. LS-associated CRC often exhibits one or more of the following features namely early age of onset, occurrence of synchronous/metachronous tumors, presence of more than one affected family member and tumors predominantly localized to the proximal/right colon with specific clinico-pathological features such as a mucinous histology, poor differentiation and immune infiltration. LS is primarily a disease of defective MisMatch Repair (MMR) and is caused by germline mutational inactivation of any one of four major MMR genes viz. MLH1, MSH2, MSH6 and PMS2. A hallmark of LS-associated tumors is presence of ‘microsatellite instability’ (MSI), a term used to describe frequent occurrence of expanded/contracted microsatellites that arise during DNA replication and are not corrected due to defective MMR. MLH1 and MSH2 account for a majority (up to 90%) of LS cases while MSH6 and PMS2 are involved in a minor proportion. Mutational inactivation of an MMR gene almost always results in loss of corresponding protein expression in the tumor, which can be easily detected by immunohistochemistry. In the first comprehensive study from India, we analyzed MSI and determined expression status of the four MMR genes in forty eight suspected LS-associated colorectal tumor samples. Though a majority (85.4%) exhibited MSI, only 58% exhibited loss of MMR expression, a significantly low proportion compared to reports from other populations. PCR-DNA sequencing and Multiple Ligation-dependent Probe Amplification based mutation and exonic deletion/duplication screening respectively, revealed MMR gene lesions in 81% of samples exhibiting loss of corresponding MMR protein expression, including thirteen mutations and four exonic rearrangements. Seven novel mutations (four in MLH1 and three in MSH2) were identified. Surprisingly, MMR gene lesions were also detected in a significant proportion (78%) of tumor samples not exhibiting MMR expression loss. Interestingly, samples with and without MMR expression exhibited significant differences with respect to mucinous histology and instability exhibited by specific microsatellites. In addition, MMR negative samples mainly harbored MMR gene in-del or point mutations while MMR positive samples predominantly harbored MMR gene exonic rearrangements. The study has therefore revealed for the first time a significant proportion of suspected LS tumors not exhibiting loss of MMR expression despite harboring MMR gene rearrangements. More importantly, our results indicate significant differences in the biology of LS-associated colorectal tumors occurring due to missense/in-del mutations in MMR genes causing loss of expression and those that occur due to MMR gene exonic rearrangements not resulting in loss of expression.

Citation Format: Murali D. Bashyam, Viswakalyan Kotapalli, Ratheesh Raman, Brijesh K. Yadav, Ajay K. Chaudhary, Swarnalata Gowrishankar, Shantveer G. Uppin, Ravikanth Kongara, Regulagadda A. Sastry, Mohana Vamsy, Sujit Patnaik, Shoba Dsouza, Devendra C. Desai, Tester Ashavaid. Identification of MMR gene exonic rearrangements in suspected Lynch syndrome tumors without loss of MMR expression. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1285. doi:10.1158/1538-7445.AM2014-1285

A positive family history of cancer or lifestyle factors may not explain the high incidence of early-onset colorectal cancer in India

SUMMARY 

Aim: Colorectal cancer (CRC) patients from developing countries such as India exhibit distinct clinico-pathological characteristics including an early age of onset and predominant tumor localization in the rectum. However, the reason(s) for increased occurrence among the young is not clear. Materials & methods: In the current study, we performed a comparative analysis of several epidemiological features in early and late-onset CRC patients from India including association with familial syndromes, diet and lifestyle habits. Results: Surprisingly, there was no significant association of any epidemiological variable with early-onset CRC. Conclusion: Perhaps low penetrance syndromes and/or other genetic causes may be responsible for an early age of onset among Indian CRC patients.

Pathological stage significantly predicts survival in colorectal cancer patients: a study from two tertiary care centers in India

SUMMARY

Aims: An increase in incidence of early-onset colorectal cancer (EOCRC) in developing countries, including India, is reported recently; however, systematic analyses of clinico-pathological features and disease prognosis has seldom been undertaken. Materials & methods: We studied clinical data pertaining to 1259 colorectal adenocarcinoma patients from two tertiary cancer centers in south India. Results: Approximately 45% of patients were aged below 50 years and poor grade and late-stage tumors were significantly associated with early disease onset. Although tumor grade and stage significantly influenced disease-free survival independently, significant association between survival and age of onset or tumor location was not detected unlike previous observations. Conclusion: Given the sizeable proportion of EOCRC, implementation of the revised Bethesda guidelines may not be tenable in India. More importantly, the previous observation of EOCRC being significantly associated with poor survival could, in part, be due to a higher proportion of advanced-stage tumors.

Splice, insertion-deletion and nonsense mutations that perturb the phenylalanine hydroxylase transcript cause phenylketonuria in India

Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by mutational inactivation of the phenylalanine hydroxylase (PAH) gene. Missense mutations are the most common PAH mutation type detected in PKU patients worldwide. We performed PAH mutation analysis in 27 suspected Indian PKU families (including 7 from our previous study) followed by structure and function analysis of specific missense and splice/insertion-deletion/nonsense mutations, respectively. Of the 27 families, disease-causing mutations were detected in 25. A total of 20 different mutations were identified of which 7 "unique" mutations accounted for 13 of 25 mutation positive families. The unique mutations detected exclusively in Indian PKU patients included three recurrent mutations detected in three families each. The 20 mutations included only 5 missense mutations in addition to 5 splice, 4 each nonsense and insertion-deletion mutations, a silent variant in coding region and a 3'UTR mutation. One deletion and two nonsense mutations were characterized to confirm significant reduction in mutant transcript levels possibly through activation of nonsense mediated decay. All missense mutations affected conserved amino acid residues and sequence and structure analysis suggested significant perturbations in the enzyme activity of respective mutant proteins. This is probably the first report of identification of a significantly low proportion of missense PAH mutations from PKU families and together with the presence of a high proportion of splice, insertion-deletion, and nonsense mutations, points to a unique PAH mutation profile in Indian PKU patients.

ARID1B, a member of the human SWI/SNF chromatin remodeling complex, exhibits tumour-suppressor activities in pancreatic cancer cell lines

Background:

The human ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) complex functions as a primary chromatin remodeler during ontogeny, as well as in adult life. Several components of the complex have been suggested to function as important regulators of tumorigenesis in various cancers. In the current study, we have characterised a possible tumour suppressor role for the largest subunit of the complex, namely the AT-rich interaction domain 1B (ARID1B).

Methods:

We performed Azacytidine and Trichostatin A treatments, followed by bisulphite sequencing to determine the possible DNA methylation-induced transcription repression of the gene in pancreatic cancer (PaCa) cell lines. Functional characterisation of effect of ARID1B ectopic expression in MiaPaCa2 PaCa cell line, which harboured ARID1B homozygous deletion, was carried out. Finally, we evaluated ARID1B protein expression in pancreatic tumour samples using immunohistochemistry on a tissue microarray.

Results:

ARID1B was transcriptionally repressed due to promoter hypermethylation, and ectopic expression severely compromised the ability of MiaPaCa2 cells to form colonies in liquid culture and soft agar. In addition, ARID1B exhibited significantly reduced/loss of expression in PaCa tissue, especially in samples from advanced-stage tumours, when compared with normal pancreas.

Conclusion:

The results therefore suggest a possible tumour-suppressor function for ARID1B in PaCa, thus adding to the growing list of SWI/SNF components with a similar function. Given the urgent need to design efficient targeted therapies for PaCa, our study assumes significance.

Abstract 1198: Presence of non-canonical tumorigenesis pathways in early-onset sporadic rectal cancer

Chromosomal instability (CIN) caused by β-Catenin dependent aberrant activation of canonical Wnt signaling or Microsatellite instability (MSI) triggered by inactivation of mismatch repair (MMR) pathway, are the two major genetic instability pathways that drive classical age-related sporadic colorectal cancer (CRC). Activation of canonical Wnt signaling and MSI are primary tumor initiating events in about 80% and 15% of late-onset CRC cases, respectively. Canonical Wnt signaling is also reported as a secondary event in tumors primarily driven by MSI. These inferences are based on seminal studies that included a disproportionately greater number of colon tumors (as compared to rectal tumors). Recent genome-wide studies have suggested colon and rectal cancer to be a single entity, though several other studies appear to indicate otherwise. Exclusive studies on rectal cancer (RC), especially the early-onset sporadic subtype, have been fewer. Despite a recent trend of increased worldwide incidence, early-onset sporadic rectal cancer (EOSRC) is not well understood. We profiled canonical Wnt, KRAS and p53 (components of the classical colorectal carcinoma progression model) and MSI status in a panel of 298 colorectal cancer samples. 41% of EOSRC samples did not harbor Wnt or MSI pathways; the high proportion of a ‘double negative’ entity was neither identified in late-onset RC samples nor in colon cancer samples. KRAS mutation frequency was also significantly lower in EOSRC (24%). Since CIN is a hallmark of canonical Wnt activation driven CRC, we profiled genome-wide DNA copy number alterations (CNAs) in microsatellite stable EOSRC samples and surprisingly identified extensive chromosomal aberrations in both Wnt active and Wnt inactive subtypes suggesting the interesting possibility of presence of CIN in the absence of canonical Wnt activation. Several CNAs were detected exclusively in Wnt inactive samples (being absent in Wnt active samples) and were validated by quantitative PCR. As expected, a few CNAs, such as an amplification detected at 17q12 (ERBB2/GRB7), were present in both subtypes. Genome-wide transcript profiling performed in parallel revealed the elevated expression of genes located within the amplifications, validated by quantitative reverse transcription PCR (Q-RT-PCR). More importantly, aberrant activation of non-canonical signaling pathways was identified in a subset of the ‘double negative’ EOSRC samples, based on unsupervised (hierarchical clustering) and supervised (significance analysis of microarrays and gene set enrichment analysis) analyses of the transcriptome data. Elevation of non-canonical pathway gene transcripts was confirmed by Q-RT-PCR. Our study has therefore revealed presence of unique tumorigenesis pathways in EOSRC samples distinct from canonical pathways that drive late-onset CRC.

Citation Format: Ratheesh Raman, Viswakalyan Kotapalli, Raju SR Adduri, Vasantha Kumar Bhaskara, Swarnalata Gowrishankar, Leena Bashyam, Ajay Chaudhary, Mohana Vamsy Chigurupati, Sujith Patnaik, Mukta Srinivasulu, Regulagadda Sastry, Subramanyeshwar Rao, Anjayneyulu Vasala, NarasimhaRaju Kalidindi, Jonathan Pollack, Sudha Murthy, Murali D. Bashyam. Presence of non-canonical tumorigenesis pathways in early-onset sporadic rectal cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1198. doi:10.1158/1538-7445.AM2013-1198

Abstract 1216: Analysis of genetic aberrations in squamous cell carcinoma of the oral tongue

Squamous cell carcinoma of the oral tongue (SCCOT) is a common form of head and neck squamous cell carcinoma (HNSCC). In the last few decades, a steady increase in incidence rates of SCCOT has been reported across the world including India. SCCOT is known to be an age related disease and tobacco consumption is implicated as the main etiological agent, like other HNSCC subtypes. Recent reports have indicated an increase in incidence of SCCOT in the young and in nonsmokers. Among HNSCC, SCCOT appears to be more aggressive with respect to its clinical and biological behavior. Molecular genetic studies on SCCOT are scarce and most studies have been conducted on a small cohort of patients and/or restricted to a single/few molecular marker(s). We have conducted a multipronged molecular genetic study of SCCOT and analyzed the status of known tumorigenesis pathways including TP53, epidermal growth factor receptor (EGFR), microsatellite instability (MSI), CDKN2A, FHIT and human papilloma virus (HPV) infection in surgically resected primary tumor samples and correlated with clinocopathological variables. 67% (67/100) of SCCOT samples exhibited p53 nuclear stabilization whereas a greater proportion (87/100; 87%) exhibited elevated EGFR expression, in accordance with existing literature. Interestingly, p53 nuclear stabilization was found to be more common in young (31/39; 79.5%) than in older (35/59; 59.3%) patients (p = 0.0481). As expected, patients with p53 nuclear stabilization exhibited poorer survival. Further, PCR based mutation screening of exons 5-8 of TP53 (encoding the DNA binding domain) revealed mutations in 50% of samples exhibiting nuclear stabilization. HPV infection was observed in 11/82 (13.4%) tumors while the frequencies of MSI (12/86; 14%) and loss of heterozygosity (LoH) in CDKN2A (32.6%) and FHIT (28.4%) loci were significantly higher than previous studies. In addition, LoH at FHIT locus was significantly associated with p53 nuclear stabilization (p=0.047). Analysis of genome-wide DNA copy number alterations (CNA) using array based comparative genomic hybridization revealed unique copy number alterations validated by quantitative PCR. Exome sequencing and transcriptome profiling are currently underway to understand the pathways/genes deregulated in SCCOT, especially in samples not exhibiting p53 nuclear stabilization.

Citation Format: Raju Sr Adduri, Viswakalyan Kotapalli, Neha Ak Gupta, Swarnalata Gowrishankar, Mukta Srinivasulu, Subramanyeshwar Rao, Shantveer G. Uppin, Umanath Karopadi Nayak, Mohana Vamsy Chigurupati, Sujith Chayu Patnaik, NarasimhaRaju Kalidindi, Murali D. Bashyam. Analysis of genetic aberrations in squamous cell carcinoma of the oral tongue. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1216. doi:10.1158/1538-7445.AM2013-1216

PNUTS functions as a proto-oncogene by sequestering PTEN

PTEN is a well-defined tumor suppressor gene that antagonizes the PI3K/Akt pathway to regulate a multitude of cellular processes, such as survival, growth, motility, invasiveness, and angiogenesis. While the functions of PTEN have been studied extensively, the regulation of its activity during normal and disease conditions still remains incompletely understood. In this study, we identified the protein phosphatase-1 nuclear targeting subunit PNUTS (PPP1R10) as a PTEN-associated protein. PNUTS directly interacted with the lipid-binding domain (C2 domain) of PTEN and sequestered it in the nucleus. Depletion of PNUTS leads to increased apoptosis and reduced cellular proliferation in a PTEN-dependent manner. PNUTS expression was elevated in certain cancers compared with matched normal tissues. Collectively, our studies reveal PNUTS as a novel PTEN regulator and a likely oncogene.

Abstract 2178: ARID1B, a member of the human SWI/SNF chromatin remodeling complex, is a novel tumor suppressor gene in pancreatic cancer

Lack of early diagnosis and efficient therapeutic options are the two major obstacles hindering improvement in pancreatic cancer (PaCa) survival rate. Traditionally, researchers have focused their attention on identification and characterization of oncogenes, given the comparative ease of therapeutic targeting. Recent studies have however suggested that up to 90% of cancer ‘driver’ genes are tumor suppressors. In our previous work, we identified a recurrent deletion located at 6q25.3 in pancreatic cancer cell lines and xenografts that included only one gene viz. ARID1B, a component of the human SWI/SNF chromatin remodeling complex. We utilized a two-pronged strategy for this study; ectopic expression in MiaPaCa2 PaCa cell line harboring an ARID1B homozygous deletion and analysis of promoter hypermethylation induced transcriptional silencing in cell lines and tumor tissues. The ARID1B cDNA was cloned into the pcDNA3.1 expression system in order to generate permanent transfectants in MiaPaCa2; vector transfectants were generated as a control. Two independent gene and vector clones were evaluated for several tumor-related characteristics. There was no significant difference in growth rates between the gene and vector clones as determined through MTT assay, crystal violet staining assay and FACS-based cell cycle analysis nor was a perceptible difference discernable in percentage apoptotic cells based on Caspase 3 and Propidium Iodide/Hoechst staining assays. However, the ARID1B clones generated significantly reduced number of colonies in liquid colony formation as well as soft agar assays indicating reduced ability to grow in the presence of contact inhibition and in the absence of anchorage, respectively. In addition, the ARID1B clones exhibited reduced motility in wound healing assays when compared to vector clones. We independently analyzed ten PaCa cell lines that exhibited a single copy loss and reduced expression of ARID1B. Azacytidine and Trichostatin A treatment resulted in a significant increase in ARID1B transcript levels indicating the possibility of methylation-induced transcriptional silencing. Bisulphite sequencing revealed extensive hypermethylation in the ARID1B promoter in cell lines exhibiting elevated transcript levels upon Azacytidine/TSA treatment but not in cell lines that exhibited no change in transcript levels. Immunohistochemistry and quantitative reverse transcription PCR-based analysis of pancreatic tumor samples revealed reduced ARID1B expression in tumour as compared to normal samples. Methylation analysis of the ARID1B promoter using DNA isolated from pancreatic cancer tissue is currently underway. Our results therefore suggest a tumor suppressor role for ARID1B in pancreatic cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2178. doi:1538-7445.AM2012-2178

A low prevalence of MYH7/MYBPC3 mutations among familial hypertrophic cardiomyopathy patients in India

Familial Hypertrophic Cardiomyopathy (FHC) is an autosomal dominant disorder affecting the cardiac muscle and exhibits varied clinical symptoms because of genetic heterogeneity. Several disease causing genes have been identified and most code for sarcomere proteins. In the current study, we have carried out clinical and molecular analysis of FHC patients from India. FHC was detected using echocardiography and by analysis of clinical symptoms and family history. Disease causing mutations in the β-cardiac myosin heavy chain (MYH7) and Myosin binding protein C3 (MYBPC3) genes were identified using Polymerase Chain Reaction-Deoxyribose Nucleic Acid (PCR-DNA) sequencing. Of the 55 patient samples screened, mutations were detected in only nineteen in the two genes; MYBPC3 mutations were identified in 12 patients while MYH7 mutations were identified in five, two patients exhibited double heterozygosity. All four MYH7 mutations were missense mutations, whereas only 3/9 MYPBC3 mutations were missense mutations. Four novel mutations in MYBPC3 viz. c.456delC, c.2128G>A (p.E710K), c.3641G>A (p.W1214X), and c.3656T>C (p.L1219P) and one in MYH7 viz. c.965C>T (p.S322F) were identified. A majority of missense mutations affected conserved amino acid residues and were predicted to alter the structure of the corresponding mutant proteins. The study has revealed a greater frequency of occurrence of MYBPC3 mutations when compared to MYH7 mutations.

SMURF1 amplification promotes invasiveness in pancreatic cancer

Pancreatic cancer is a deadly disease, and new therapeutic targets are urgently needed. We previously identified DNA amplification at 7q21-q22 in pancreatic cancer cell lines. Now, by high-resolution genomic profiling of human pancreatic cancer cell lines and human tumors (engrafted in immunodeficient mice to enrich the cancer epithelial fraction), we define a 325 Kb minimal amplicon spanning SMURF1, an E3 ubiquitin ligase and known negative regulator of transforming growth factor β (TGFβ) growth inhibitory signaling. SMURF1 amplification was confirmed in primary human pancreatic cancers by fluorescence in situ hybridization (FISH), where 4 of 95 cases (4.2%) exhibited amplification. By RNA interference (RNAi), knockdown of SMURF1 in a human pancreatic cancer line with focal amplification (AsPC-1) did not alter cell growth, but led to reduced cell invasion and anchorage-independent growth. Interestingly, this effect was not mediated through altered TGFβ signaling, assayed by transcriptional reporter. Finally, overexpression of SMURF1 (but not a catalytic mutant) led to loss of contact inhibition in NIH-3T3 mouse embryo fibroblast cells. Together, these findings identify SMURF1 as an amplified oncogene driving multiple tumorigenic phenotypes in pancreatic cancer, and provide a new druggable target for molecularly directed therapy.

Abstract 3766: Low frequency of MLH1/MSH2 inactivation in suspected HNPCC patients from India

Hereditary Non-Polyposis Colorectal Cancer (HNPCC) is an autosomal dominant familial syndrome resulting in colorectal cancer at a young age. It is caused mainly due to germline mutational inactivation of any one of four mismatch repair (MMR) genes viz. MSH2, MLH1, MSH6 and PMS2 resulting in the ‘mutator’ phenotype called microsatellite instability (MSI). The mutations often result in loss of protein expression which can be detected using immunohistochemistry (IHC). IHC and MSI analysis have been suggested as pre-screening methods for selection of patients for mutation analysis of MMR genes. Studies from several populations have indicated that MLH1/MSH2 inactivation may account for a majority of HNPCC cases. We earlier reported unique clinico-pathological and molecular genetic features in Indian sporadic colorectal cancer patients. We have now carried out a multi pronged analysis of suspected HNPCC patients from India. MSI screening and IHC for MLH1 and MSH2 followed by mutation analysis was employed on a panel of Indian CRC patients who were aged below 50 years at the time of diagnosis and exhibited HNPCC-specific family history. We also included patients who had multiple primary tumors or were of older age but exhibited HNPCC-specific familial involvement. As expected, a significant majority of patients (upto 80%) harbored tumors exhibiting high MSI (MSI-H) as compared to young patients without family history (only upto 20%). Surprisingly, a significantly low proportion (only about 30%) of young patients positive for family history and MSI-H exhibited loss of MLH1/MSH2 expression, perhaps due to mutations not resulting in loss of protein expression or the involvement of MSH6/PMS2 in Indian patients at a frequency higher than other populations. IHC for MSH6/PMS2 is currently underway. Mutation screening for the appropriate gene was carried out in eight patients negative for IHC using genomic DNA isolated from blood samples. Six heterozygous germline mutations (including four novel mutations) were identified; three each in MLH1 and MSH2. Studies are ongoing to determine whether the second allele in each of the six cases was inactivated through loss of heterozygosity. Interestingly, all patients in whom mutation was identified harbored tumor in the ascending colon. Three of the six mutations generate premature termination codons expected to trigger nonsense mediated decay resulting in reduced transcript levels of the respective genes. A fourth mutation (in MLH1) resulted in drastic reduction in transcript levels as determined by quantitative reverse transcription polymerase chain reaction; no such reduction was discernable in a microsatellite stable sporadic CRC sample. Analysis of effect of the remaining two mutations is currently underway. Our results therefore reveal unique features in Indian HNPCC patients; IHC for MLH1/MSH2 may not be an ideal primary screening tool to identify HNPCC patients in India.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3766. doi:10.1158/1538-7445.AM2011-3766

Phenylalanine hydroxylase gene mutations in phenylketonuria patients from India: identification of novel mutations that affect PAH RNA

Analysis of seven Indian phenylketonuria families has revealed four novel mutations in the phenylalanine hydroxylase gene; two affected consensus splice sequence and the 3' UTR, respectively, while the other two were single base insertion and deletion mutations, respectively. A novel 3' splice site mutation c.168-2A>G resulted in the activation of a cryptic 3' splice site that generated a premature termination codon leading to very low levels of the mutant transcript, probably due to activation of the nonsense-mediated decay (NMD) pathway. This is probably the first report of PKU caused by the activation of NMD.

Abstract 5017: Identification and characterization of tumor suppressor genes located within chromosomal regions frequently deleted in pancreatic cancer

Genome-wide transcript profiling has been frequently used to aid prognostication in cancers that exhibit extensive heterogeneity in their clinical presentation. For cancers that are consistently associated with a high mortality rate such as pancreatic cancer, it is more relevant to design efficient therapeutic strategies. DNA copy number alterations are expected to harbor deregulated oncogenes and tumor suppressor genes (TSGs) important for maintaining the tumor phenotype, which in turn may yield novel therapeutic targets. We earlier carried out array-based comparative genomic hybridization on a panel of pancreatic cancer cell lines and xenografts and identified GATA6 as a novel lineage specific deregulated oncogene. In the current study, we have characterized two recurrent deletions; one located at 6q25.3 and the other at 18q23. Careful analysis of genes located within the 6q25.3 deletion revealed only two genes, one of which, ARID1B, is a component of the human SWI/SNF complex. The gene was cloned in pCDNA3.1His vector and transiently transfected into the pancreatic cancer cell line MiaPaCa2 harboring a homozygous deletion of ARID1B. FACS analysis revealed no significant change in S-phase fraction of cells when compared to results obtained with the vector alone. A stable ARID1B expression clone was generated in MiaPaCa2; gene expression was confirmed using reverse transcription (RT) PCR. Colony forming assay revealed a significant reduction in the size and number of colonies formed by the ARID1B stable clone as compared to the vector stable clone indicating that expression of ARID1B could alleviate tumor-related phenotype in pancreatic cancer cell lines. Azacytidine treatment in SW1990, a pancreatic cancer cell line harboring a single copy loss of ARID1B and exhibiting low expression, appeared to alleviate transcriptional repression indicating that the gene may be regulated through promoter hypermethylation in pancreatic cancer cells. RT-PCR analysis has revealed the authentic transcript isoform of ARID1B in pancreatic cancer. Analysis of another recurrent deletion located at 18q23 revealed the PARD6G gene as the possible TSG in this locus. PARD6G is a component of the cell polarity complex and is expected to regulate cell motility. Analysis of DNA copy number and transcript levels of PARD6G in various pancreatic cell lines and xenografts revealed a strong concordance. The gene exhibited a single copy loss in several pancreatic cancer cell lines; Bisulphite sequencing analysis revealed strong hypermethylation of CpG islands spanning the first intron in the remaining allele. Further studies are underway to determine the role played by ARID1B and PARD6G in pancreatic cancer progression.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5017.

The MYH7 p.R787H mutation causes hypertrophic cardiomyopathy in two unrelated families

BACKGROUND

Familial hypertrophic cardiomyopathy (FHC) is a Mendelian disorder usually caused by mutations in any one of more than 12 genes, most of which encode sarcomere proteins. The disease exhibits extensive genetic heterogeneity, and it is important to identify mutations that result in adverse symptoms and/or lethality in affected individuals. An analysis of disease-causing mutations has been initiated in the Indian population to determine prevalent mutations.

METHODS

FHC was detected using echocardiography and by analysis of clinical symptoms and family history. The disease-causing mutation was identified using polymerase chain reaction DNA sequencing.

RESULTS

The p.R787H mutation was identified in the MYH7 gene in two FHC families. Sequence and structure analysis suggested impaired binding of the mutant protein to the myosin essential light chain.

CONCLUSIONS

Although the mutation results in variable clinical symptoms in the affected individuals, probably owing to the effect of modifier genes and/or environmental factors, it does not appear to be a lethal mutation.

A p.R870H mutation in the beta-cardiac myosin heavy chain 7 gene causes familial hypertrophic cardiomyopathy in several members of an Indian family

Familial hypertrophic cardiomyopathy is an autosomal dominant genetic disorder characterized mainly by left ventricular hypertrophy and myocyte disarray; it is the most common cause of sudden death in otherwise healthy individuals. More than 270 mutations in genes encoding the cardiac sarcomere have been identified. Attempts to establish a genotype-phenotype correlation for each of the mutations have not been highly successful. It has been suggested that additional genetic loci, as well as nongenetic factors such as lifestyle, gender and age, may play a role in modulating the clinical presentation of the disease. The p.R870H mutation has been identified as the cause of familial hypertrophic cardiomyopathy in an Indian family. The results indicate that the disease phenotype varied among various affected members of the family, and the variation may be attributed to factors, such as gender and gene dosage.

Array-based comparative genomic hybridization identifies localized DNA amplifications and homozygous deletions in pancreatic cancer

Pancreatic cancer, the fourth leading cause of cancer death in the United States, is frequently associated with the amplification and deletion of specific oncogenes and tumor-suppressor genes (TSGs), respectively. To identify such novel alterations and to discover the underlying genes, we performed comparative genomic hybridization on a set of 22 human pancreatic cancer cell lines, using cDNA microarrays measuring approximately 26,000 human genes (thereby providing an average mapping resolution of <60 kb). To define the subset of amplified and deleted genes with correspondingly altered expression, we also profiled mRNA levels in parallel using the same cDNA microarray platform. In total, we identified 14 high-level amplifications (38-4934 kb in size) and 15 homozygous deletions (46-725 kb). We discovered novel localized amplicons, suggesting previously unrecognized candidate oncogenes at 6p21, 7q21 (SMURF1, TRRAP), 11q22 (BIRC2, BIRC3), 12p12, 14q24 (TGFB3), 17q12, and 19q13. Likewise, we identified novel polymerase chain reaction-validated homozygous deletions indicating new candidate TSGs at 6q25, 8p23, 8p22 (TUSC3), 9q33 (TNC, TNFSF15), 10q22, 10q24 (CHUK), 11p15 (DKK3), 16q23, 18q23, 21q22 (PRDM15, ANKRD3), and Xp11. Our findings suggest candidate genes and pathways, which may contribute to the development or progression of pancreatic cancer.

The extracytoplasmic function sigma factors: role in bacterial pathogenesis

Bacteria utilize a distinct subfamily of sigma factors to regulate extra cytoplasmic function (thus termed as ECF subfamily). Eubacteria appear to have evolved to incorporate extensive genetic diversity into their repertoire of ECF sigma factors (some species have more than 60 ECF sigma factors), while maintaining three major themes common to all members including: (1) they regulate and respond to extracytoplasmic functions; (2) they are themselves regulated by anti-sigma and/or anti-anti-sigma factors; and (3) most of them control a relatively small regulon. The cell wall is the first bacterial structure that comes in contact with the host during infection by pathogenic bacteria. The cell wall components are often associated with functions related to host cell invasion. It is therefore, likely that the ECF sigma factors regulate the bacterial response to host insult. Moreover, in some cases, virulence factors have been shown to be regulated directly by the ECF sigma factors. Unfortunately, this facet of the ECF sigma factors has not been an important area of study by researchers. The present review attempts to highlight the important role played by ECF sigma factors in bacterial pathogenesis and highlights several areas of future study involving the genetics of ECF sigma factors vis-à-vis bacterial pathogenesis.

The homologous region sequence (hr1) of Autographa californica multinucleocapsid polyhedrosis virus can enhance transcription from non-baculoviral promoters in mammalian cells

The Autographa californica multinucleocapsid polyhedrosis virus homologous region sequence hr1 enhances transcription from the viral polyhedrin promoter in Spodoptera frugiperda insect cells and independently functions as an origin of replication (ori) sequence. The binding of the host nuclear protein, hr1-binding protein (hr1-BP), is crucial for the enhancer activity (Habib, S., Pandey, S., Chatterji, U., Burma, S., Ahmad, R., Jain, A., and Hasnain, S. E. (1996) DNA Cell Biol. 15, 737-747 and Habib, S., and Hasnain, S. E. (1996) J. Biol. Chem. 271, 28250-28258). We demonstrate that hr1 can also enhance transcription from non-baculoviral promoters like cytomegalovirus and hsp70 in mammalian cells but does not support ori activity in these cells. Unlike insect cells, hr1 can also function in mammalian cells as an enhancer when present in trans. hr1 DNA sequence binds with high affinity and specificity to nuclear factors in the mammalian cells. The insect hr1-BP- and the hr1-BP-like proteins from mammalian cells (mhr1-BP) have different properties with respect to ion requirements, DNA groove binding, and molecular size. When mammalian cells are infected with a recombinant baculovirus containing two promoters, the baculovirus polyhedrin and Drosophila hsp70 gene promoter, the hsp70 gene promoter alone is active in these cells, and this activity is further enhanced by the presence of an additional hr1 in the recombinant virus. hr1 may thus also have a role in baculovirus-mediated gene delivery in mammalian cells.

Molecular genetics of familial hypertrophic cardiomyopathy (FHC)

Familial hypertrophic cardiomyopathy is an autosomal dominant disease with a wide range of clinical features from benign to severe, and is the most common cause of sudden death in otherwise healthy individuals. The two prominent clinical features are left ventricular hypertrophy and myocyte/myofibrillar disarray. The former is responsible for clinical symptoms such as breathlessness and angina, whereas the latter may lead to sudden cardiac death. The last decade has seen an enormous improvement in our understanding of the molecular genetics of this disorder. The clinical heterogeneity has been linked to genetic heterogeneity; mutations in nine genes encoding sarcomere proteins have been shown to be the molecular basis for the disorder. However, attempts to establish a genotype-phenotype correlation for each of the more than 100 mutations that have been identified have not been highly successful. Additional genetic loci, as well as nongenetic factors such as lifestyle, sex, and age, have also been shown to play a role in modulating the clinical presentation of the disease. How each mutation results in hypertrophy and/or myofibrillar disarray is unclear. The present review discusses the current status of the molecular genetic characterization of this important disorder.

The human genome sequence: impact on health care

The recent sequencing of the human genome, resulting from two independent global efforts, is poised to revolutionize all aspects of human health. This landmark achievement has also vindicated two differeint methodologies that can now be used to target other important large genomes. The human genome sequence has revealed several novel/surprising features notably the probable presence of a mere 30-35,000 genes. In depth comparisons have led to classification of protein families and identification of several orthologues and paralogues. Information regarding non-protein coding genes as well as regulatory regions has thrown up several new areas of research. Although still incomplete, the sequence is poised to become a boon to pharmaceutical companies with the promise of delivering several new drug targets. Several ethical concerns have also been raised and need to be addressed in earnest. This review discusses all these aspects and dwells on the possible impact of the human genome sequence on human health, medicine and also health care delivery system.

Understanding cancer metastasis: an urgent need for using differential gene expression analysis

Cancer is a multistep process and occurs as a result of the loss of control of cell division, leading to the initial tumor formation, which is followed by metastatic spread. Recent years have witnessed a vast improvement in the understanding of the molecular mechanisms regulating cell division and their links to tumorigenesis. The process of metastasis involves an intricate interplay between cell adhesion, proteolysis, migration, and angiogenesis. However, there is little knowledge of how these events are coordinately regulated in the tumor cell. Given that the uncontrolled spread of the tumor to distant organs is usually lethal, a study of the molecular mechanisms regulating metastasis assumes great significance. Recently, several technologies have been developed for analyzing differential gene expression. The current review discusses the importance of these technologies in the molecular analyses of metastasis.

Novel Sp family-like transcription factors are present in adult insect cells and are involved in transcription from the polyhedrin gene initiator promoter

We earlier documented the involvement of a cellular factor, polyhedrin (polh) promoter-binding protein, in transcription from the Autographa californica nuclear polyhedrosis virus polh gene promoter. Sequences upstream of the polh promoter were found to influence polh promoter-driven transcription. Analysis of one such region, which could partially compensate for the mutated polh promoter and also activate transcription from the wild-type promoter, revealed a sequence (AcSp) containing a CACCC motif and a loose GC box resembling the binding motifs of the transcription factor Sp1. AcSp and the consensus Sp1 sequence (cSp) specifically bound factor(s) in HeLa and Spodoptera frugiperda (Sf9) insect cell nuclear extracts to generate identical binding patterns, indicating the similar nature of the factor(s) interacting with these sequences. The AcSp and cSp oligonucleotides enhanced in vivo expression of a polh promoter-driven luciferase gene. In vivo mopping of these factor(s) significantly reduced transcription from the polh promoter. Recombinant viruses carrying deletions in the upstream AcSp sequence confirmed the requirement of these factor(s) in polh promoter-driven transcription in the viral context. We demonstrate for the first time DNA-protein interactions involving novel members of the Sp family of proteins in adult insect cells and their involvement in transcription from the polh promoter.

Identification and analysis of "extended -10" promoters from mycobacteria

Earlier studies from our laboratory on randomly isolated transcriptional signals of mycobacteria had revealed that the -10 region of mycobacterial promoters and the corresponding binding domain in the major sigma factor are highly similar to their Escherichia coli counterparts. In contrast, the sequences in -35 regions of mycobacterial promoters and the corresponding binding domain in the major sigma factor are vastly different from their E. coli counterparts (M. D. Bashyam, D. Kaushal, S. K. Dasgupta, and A. K. Tyagi, J. Bacteriol. 178:4847-4853, 1996). We have now analyzed the role of the TGN motif present immediately upstream of the -10 region of mycobacterial promoters. Sequence analysis and site-specific mutagenesis of a Mycobacterium tuberculosis promoter and a Mycobacterium smegmatis promoter reveal that the TGN motif is an important determinant of transcriptional strength in mycobacteria. We show that mutation in the TGN motif can drastically reduce the transcriptional strength of a mycobacterial promoter. The influence of the TGN motif on transcriptional strength is also modulated by the sequences in the -35 region. Comparative assessment of these extended -10 promoters in mycobacteria and E. coli suggests that functioning of the TGN motif in promoters of these two species is similar.

A study of mycobacterial transcriptional apparatus: identification of novel features in promoter elements

Our earlier studies on transcriptional signals of mycobacteria had revealed that (i) strong promoters occur less frequently in the slowly growing pathogen Mycobacterium tuberculosis H37Rv than in the fast-growing saprophyte M. smegmatis and (ii) mycobacterial promoters function poorly in Escherichia coli. We now present evidence that RNA polymerases of M. smegmatis, M. tuberculosis, and M. bovis BCG recognize promoter elements with comparable efficiencies. Analysis of these randomly isolated mycobacterial promoters by DNA sequencing, primer extension, and deletion experiments revealed that their -10 regions are highly similar to those of E. coli promoters, in contrast to their -35 regions, which can tolerate a greater variety of sequences, owing presumably to the presence of multiple sigma factors with different or overlapping specificities for -35 regions, as reported earlier for the Streptomyces promoters. A comparison of the -10 and -35 binding domains of MysA, HrdB, and RpoD (the principal sigma factors of M. smegmatis, Streptomyces aureofaciens, and E. coli, respectively) showed that all three sigma factors have nearly identical -10 binding domains. However, the -35 binding domains of the principal mycobacterial and streptomycete sigma factors, although nearly identical to each other, are vastly different from the corresponding region of the sigma factor of E. coli. Thus, the transcriptional signals of mycobacteria have features in common with Streptomyces promoters but differ from those of E. coli because of major differences in the -35 regions of the promoters and the corresponding binding domain in the sigma factor.

Cloning and assessment of mycobacterial promoters by using a plasmid shuttle vector

We have constructed a promoter selection vector for mycobacteria to analyze the sequences involved in mycobacterial transcriptional regulation. The vector pSD7 contains extrachromosomal origins of replication from Escherichia coli as well as from Mycobacterium fortuitum and a kanamycin resistance gene for positive selection in mycobacteria. The promoterless chloramphenicol acetyltransferase (CAT) reporter gene has been used to detect mycobacterial promoter elements in a homologous environment and to quantify their relative strengths. Using pSD7, we have isolated 125 promoter clones from the slowly growing pathogen Mycobacterium tuberculosis H37Rv and 350 clones from the fast-growing saprophyte Mycobacterium smegmatis. The promoters exhibited a wide range of strengths, as indicated by their corresponding CAT reporter activities (5 to 2,500 nmol/min/mg of protein). However, while most of the M. smegmatis promoters supported relatively higher CAT activities ranging from 100 to 2,500 nmol/min/mg of protein, a majority of those from M. tuberculosis supported CAT activities ranging from 5 to only about 100 nmol/min/mg of protein. Our results indicate that stronger promoters occur less frequently in the case of M. tuberculosis compared with M. smegmatis. To assess the extent of divergence of mycobacterial promoters vis-à-vis those of E. coli, the CAT activities supported by the promoters in E. coli were measured and compared with their corresponding activities in mycobacteria. Most of the mycobacterial promoter elements functioned poorly in E. coli. The homologous selection system that we have developed has thus enabled the identification of mycobacterial promoters that apparently function optimally only in a native environment.