Chunbo Shao

Johns Hopkins University, Otolaryngology, Post-Doc

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Supervisors: Melanie Ehrlich and Patrick Ha
Phone: 410-807-5213

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Books by Chunbo Shao

Finding genes where you did not expect them

What’s a gene? Where are the DNA elements that turn genes on and off? These issues, which many ... more What’s a gene? Where are the DNA
elements that turn genes on and
off? These issues, which many thought
were well on their way to being understood,
are now wide open again with
the increasing demonstration of DNA
being copied into RNA from unexpected
places in the human genome. Sometimes
this means the “wrong” strand of
double-stranded DNA being copied in
addition to the correct strand that
codes for a protein. The product of
wrong-strand copying, logically
enough, is called antisense RNA, as
compared to the sense RNA that codes
for proteins.

Do You Know What It Means To Miss New Orleans?

After cooking all of the food in our freezer and packing most of the food in the refrigerator o... more After cooking all of the food in our
freezer and packing most of the
food in the refrigerator on Sunday
morning, August 28, 2005, we left for
my lab and office on the fourth floor of
Tulane Medical School
in the afternoon. This
was our fifth evacuation
there since 1972
prompted by a hurricane
alert. We brought
some clothes, our foam
sleeping mattress, some
sheets and towels, flashlights,
and Monopoly,
which had served us
well previously as a way
to ease the tension of
these hurricane alerts.
From phone calls and
email messages before
Tulane’s server was
shut down on Saturday, I knew that all
my students and postdocs had safely
evacuated.

FSHD molecular diagnosis flowchart now available

An excellent paper published in the journal Chromosoma and coauthored by FSH Society grantees Mel... more An excellent paper published in the
journal Chromosoma and coauthored
by FSH Society grantees Melanie
Ehrlich, Ph.D. and Richard Lemmers,
MSc., Ph.D., introduced improvements to
genetic testing and education in genetic
testing for FSHD. Their article contains
one of the finest graphic depictions of a
flowchart of recommended procedures for
molecular diagnosis for FSHD.
The paper illustrates “the inherent
complexity of FSHD molecular diagnosis
due to the 4q and 10q homology between
D4Z4 arrays and adjacent sequences,
translocations between 4q and 10q D4Z4
arrays, mitotic D4Z4 contractions, deletions
encompassing p13E-11, and the wide
range of sizes of D4Z4 arrays combined
with the need for high resolution of bands
in the 30- to 45-kb range.” They also
make an improvement to the genetic testing
for FSHD. “An important advantage of
using a D4Z4 probe for molecular diagnosis
of FSHD in conjunction with the p13E-
11 probe is that it permits the
identification of about 3% of FSHD
patients who have a deletion of the p13E-
11 genomic sequence next to a short 4q
D4Z4 array (Lemmers et al. 2003).”
The article is an excellent overview of
the state-of-the-art complex genetics of
FSHD. In particular, figure 6 on page 114
has a long-overdue flowchart for the
molecular diagnosis of FSHD. It depicts
testing scenarios for both confirmation of
clinical FSHD as well as exclusion to
prove no clinical FSHD. Many thanks go to Drs. Ehrlich and
Lemmers and co-authors for this significant
improvement in both genetic tests for
FSHD as well as providing materials and
documentation of how FSHD genetic testing
works for the un-indoctrinated genetic
testing centers and counselors.

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Papers by Chunbo Shao

A novel siRNA–gemcitabine construct as a potential therapeutic for treatment of pancreatic cancer

NAR Cancer, 2020

The non-nucleoside analog gemcitabine has been the standard of care for treating pancreatic cance... more The non-nucleoside analog gemcitabine has been the standard of care for treating pancreatic cancer. The drug shows good potency in pancreatic cancer cells in vitro but, due to poor bioavailability, requires administration in large doses by infusion and this systemic exposure results in significant toxicity for the patient. Genes have been identified that, when silenced by siRNA, synergize with gemcitabine treatment and offer a means of reducing the gemcitabine dosage required for efficacy. However, benefiting from the synergism between the two agents requires that the gemcitabine and siRNA penetrate the same cells. To ensure co-delivery, we incorporated gemcitabine covalently within siRNAs against targets synergistic with gemcitabine (CHK1 or RAD17). We demonstrated that specific bases within an siRNA can be replaced with gemcitabine to increase efficacy. The result is a single drug molecule that simultaneously co-delivers gemcitabine and a synergistic siRNA. The siRNA–gemcitabine c...

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Abstract 3983: Highly sensitive detection of MYB-NFIB fusion transcripts in adenoid cystic carcinoma

Cancer Research, 2016

Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA In recent years, ... more Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA In recent years, the understanding of genomic events underlying head and neck cancer has significantly advanced. Several of the newly discovered genomic aberrations observed in salivary gland neoplasms were found to be recurrent and uniquely associated with specific disease entities. Adenoid cystic carcinoma (ACC), one of the most common salivary gland malignancies, demonstrates a particular challenge in head and neck oncology due its relentless growth, high local recurrence rate and poor long-term prognosis. Recent identification of the MYB-NFIB gene fusion as a recurrent and pathognomonic feature of ACC created new opportunities for the molecular diagnostics of this malignancy. Liquid biopsy techniques coupled with droplet digital PCR (ddPCR) platform may be feasible aiming for non-invasive detection of disease-specific genetic markers such as gene fusions. Given the prevalence of MYB-NFIB transcript in ACC, detection of the fusion event in patients’ saliva may present a unique opportunity for an accurate diagnostics as well as for long-term patient monitoring. Our goal is to develop a highly-sensitive ddPCR-based assay that would precisely detect and identify MYB-NFIB transcripts in tumor tissue and patients’ bodily fluids. RNA sequencing (RNAseq) performed in fresh frozen ACC samples identified MYB-NFIB fusion in 56% (10/18) of the cases and revealed large variability in MYB gene break sites and alternative splicing of NFIB component. 84% of ACC cases demonstrated high expression of 5’ MYB fragment by ddPCR based RT-PCR, 62.5% of which were MYB-NFIB fusion positive in RNAseq. We developed a panel of RT-PCR assays to detect a range of different MYB-NFIB transcripts observed by our RNAseq data and/or previously reported. We identified all ACC cases harboring the most commonly reported MYB-NFIB fusions (9/9) and validated the fusion products with conventional Sanger sequencing. Additionally, our preliminary results indicate that the assays are feasible for PCR multiplexing retaining the high sensitivity and specificity observed in singleplex experiments. Evaluation of the assay performance in ddPCR and assessing the detection limit is currently in progress. Once the methodology is validated, we will be able to evaluate a cohort of salivary gland neoplasms and matched RNA samples isolated from saliva. The detection of MYB-NFIB fusion in bodily fluids using a highly sensitive ddPCR platform will open a new avenue for the diagnosis and the clinical management of patients with ACC. Furthermore, our work creates the possibility of a liquid biopsy-based detection of other disease-specific gene fusions increasingly identified in different solid tumors. Citation Format: Piotr T. Wysocki, Shizhang Ling, Chunbo Shao, Marietta Tan, David Sidransky, Patrick Ha, Mariana Brait. Highly sensitive detection of MYB-NFIB fusion transcripts in adenoid cystic carcinoma. [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 3983.

Zhong X Hypermethylation in Shistosoma Haematobium infection PLOSone 2013

Value of chest CT in the diagnosis and management of tracheobronchial foreign bodies

Pediatrics International, 2011

Background: The aim of the present study was to investigate the value of chest multidetector comp... more Background: The aim of the present study was to investigate the value of chest multidetector computed tomography (CT) in the evaluation of children with suspected foreign body aspiration. Methods: Chest CT was performed in 45 consecutive children with suspected foreign body aspiration, and plain chest X-ray was conducted at the same time. Multiplanar reformatted imaging was carried out after multidetector CT. Rigid bronchoscopy and removal of the foreign body was performed under general anesthesia. Results: All 42 patients (100%) with tracheobronchial foreign bodies were identified on chest CT. Three patients avoided unnecessary operations due to negative CT scans. For the patients with tracheobronchial foreign bodies, the occurrence of unilateral hyperlucent lung and post-obstructive lobar or segmental infiltrates on plain chest X-ray was 42.9% (18/42) and 4.8% (2/42), respectively. Twenty-two of the 42 patients (52.4%) had no abnormalities on plain X-ray. The difference between multidetector CT and plain X-ray results was statistically significant (P < 0.001). Surgical plans were designed and appropriate foreign body forceps were selected based on the CT scans. All foreign bodies were removed successfully, and no severe complications were observed. The location, shape, and volume of the foreign bodies found at surgery were consistent with the CT images. Conclusions: The diagnosis of foreign body aspiration of the airway in children can be accomplished by using chest multidetector CT. It is often useful in delineating the exact shape, location, volume and form of a bronchial foreign body and can help the surgeon plan for operative bronchoscopy and safe removal of the foreign body.

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To "grow" or "go": TMEM16A expression as a switch between tumor growth and metastasis in SCCHN

Clinical cancer research : an official journal of the American Association for Cancer Research, 2014

Tumor metastasis is the leading cause of death in patients with cancer. However, the mechanisms t... more Tumor metastasis is the leading cause of death in patients with cancer. However, the mechanisms that underlie metastatic progression remain unclear. We examined TMEM16A (ANO1) expression as a key factor shifting tumors between growth and metastasis. We evaluated 26 pairs of primary and metastatic lymph node (LN) tissue from patients with squamous cell carcinoma of the head and neck (SCCHN) for differential expression of TMEM16A. In addition, we identified mechanisms by which TMEM16A expression influences tumor cell motility via proteomic screens of cell lines and in vivo mouse studies of metastasis. Compared with primary tumors, TMEM16A expression decreases in metastatic LNs of patients with SCCHN. Stable reduction of TMEM16A expression enhances cell motility and increases metastases while decreasing tumor proliferation in an orthotopic mouse model. Evaluation of human tumor tissues suggests an epigenetic mechanism for decreasing TMEM16A expression through promoter methylation that ...

Quantitative Methylation Profiles for Multiple Tumor Suppressor Gene Promoters in Salivary Gland Tumors

PLoS ONE, 2010

Mitochondrial Mutations in Adenoid Cystic Carcinoma of the Salivary Glands

PLoS ONE, 2009

Aquaporin-1 Promoter Hypermethylation Is Associated with Improved Prognosis in Salivary Gland Adenoid Cystic Carcinoma

Otolaryngology–Head and Neck Surgery, 2014

Objectives Aquaporin-1 (AQP1) is a candidate oncogene that is epigenetically modified in adenoid ... more Objectives Aquaporin-1 (AQP1) is a candidate oncogene that is epigenetically modified in adenoid cystic carcinoma (ACC). We sought to (1) assess AQP1 promoter methylation and expression in an ACC cohort, (2) identify correlations between AQP1 and clinical outcomes, and (3) explore the role of AQP1 in tumor progression in vitro. Study design Laboratory study, retrospective chart review. Setting Academic medical center. Methods DNA and RNA were isolated from ACC tumors and control salivary gland tissues. Quantitative methylation-specific polymerase chain reaction (PCR) was performed on bisulfite-treated DNA. Quantitative reverse transcription PCR was performed after cDNA synthesis. Cell lines stably overexpressing an AQP1 plasmid or empty vector were generated. Cell scratch and Matrigel invasion assays were performed. Retrospective chart review was performed for collection of clinical information. Results Methylation results from 77 tumors and 30 controls demonstrated that AQP1 was hy...

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Increased Aquaporin-1 Expression Is Associated with Improved Prognosis in Salivary Gland Adenoid Cystic Carcinoma

Otolaryngology -- Head and Neck Surgery, 2013

Objectives: Aquaporin-1 (AQP1) is a candidate oncogene that is epigenetically modified in adenoid... more Objectives: Aquaporin-1 (AQP1) is a candidate oncogene that is epigenetically modified in adenoid cystic carcinoma (ACC). We sought to 1) assess AQP1 promoter methylation and gene expression in an ACC cohort, 2) identify correlations between AQP1 and clinical outcomes, and 3) explore the role of AQP1 in tumor progression in vitro. Methods: DNA and RNA were isolated from ACC tumors and control salivary gland tissues. Quantitative methylation-specific polymerase chain reaction (PCR) was performed on bisulfite-treated DNA. Quantitative reverse transcription PCR was performed after cDNA synthesis. Retrospective chart review was performed for collection of demographic information and clinical outcomes. Cell lines stably over-expressing an AQP1 plasmid or empty vector were generated. Cell scratch and Matrigel invasion assays were then performed. Results: Methylation results from 77 ACC tumors and 30 controls demonstrated that AQP1 was hypomethylated in tumors (P < 0.0001). Fifty-eight tumors (75.3%) displayed AQP1 hypomethylation compared to controls. AQP1 expression was assessed in 58 tumors and 23 controls, and a trend towards increased expression in tumors was found (P = 0.08). Statistical analysis revealed no associations between AQP1 methylation status and clinical outcomes. However, increased AQP1 expression was associated with improved overall survival and longer time to metastasis (P < 0.05). AQP1 over-expression in vitro did not affect cell migratory or invasive capacities in cell scratch and invasion assays. Conclusions: AQP1 hypomethylation is common in ACC, and AQP1 tends to be over-expressed in these tumors. Increased AQP1 expression is associated with improved prognosis. Further in vitro studies are necessary to clarify the role of AQP1 in ACC progression.

Evaluation of MYB promoter methylation in salivary adenoid cystic carcinoma

Oral Oncology, 2011

The transcription factor MYB was recently proposed to be a promising oncogene candidate in saliva... more The transcription factor MYB was recently proposed to be a promising oncogene candidate in salivary gland adenoid cystic carcinoma (ACC). However, the up-regulation of MYB in ACC could not be explained solely by deletion of its 3′ end. It is widely accepted that the promoter methylation status can regulate the transcription of genes, especially in human cancers. Therefore, it is important to know whether MYB promoter demethylation could explain the over-expression of MYB in ACC. By using the Methprimer program, we identified nine CpG islands in the promoter of MYB. All of these CpG islands were located within the -864 to +2,082 nt region relative to the transcription start site of MYB. We then used bisulfite genomic sequencing to evaluate the methylation levels of the CpG islands of MYB in 18 primary ACC tumors, 13 normal salivary gland tissues and nine cancer cell lines. Using cell lines, we also determined the relative MYB expression levels and correlated these with the methylation levels. With bisulfite genomic sequencing, we found no detectable methylation in the CpG islands of MYB in either ACC or normal salivary gland tissues. There was a variable degree of MYB expression in the cell lines tested, but none of these cell lines demonstrated promoter methylation. Promoter hypomethylation does not appear to explain the differential expression of MYB in ACC. An alternative mechanism needs to be proposed for the transcriptional control of MYB in ACC.

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Targeting Aberrant DNA Double-Strand Break Repair in Triple-Negative Breast Cancer with Alpha-Particle Emitter Radiolabeled Anti-EGFR Antibody

Molecular Cancer Therapeutics, 2013

The higher potential efficacy of alpha-particle radiopharmaceutical therapy lies in the 3-to 8-fo... more The higher potential efficacy of alpha-particle radiopharmaceutical therapy lies in the 3-to 8-fold greater relative biological effectiveness (RBE) of alpha particles relative to photon or beta-particle radiation. This greater RBE, however, also applies to normal tissue, thereby reducing the potential advantage of high RBE. As alpha particles typically cause DNA double-strand breaks (DSB), targeting tumors that are defective in DSB repair effectively increases the RBE, yielding a secondary, RBE-based differentiation between tumor and normal tissue that is complementary to conventional, receptor-mediated tumor targeting. In some triplenegative breast cancers (TNBC; ER À /PR À /HER-2 À), germline mutation in BRCA-1, a key gene in homologous recombination DSB repair, predisposes patients to early onset of breast cancer. These patients have few treatment options once the cancer has metastasized. In this study, we investigated the efficacy of alpha-particle emitter, 213 Bi-labeled anti-EGF receptor antibody, cetuximab, in BRCA-1-defective TNBC. 213 Bi-cetuximab was found to be significantly more effective in the BRCA-1-mutated TNBC cell line HCC1937 than BRCA-1competent TNBC cell MDA-MB-231. siRNA knockdown of BRCA-1 or DNA-dependent protein kinase, catalytic subunit (DNA-PKcs), a key gene in non-homologous end-joining DSB repair pathway, also sensitized TNBC cells to 213 Bi-cetuximab. Furthermore, the small-molecule inhibitor of DNA-PKcs, NU7441, sensitized BRCA-1-competent TNBC cells to alpha-particle radiation. Immunofluorescent staining of g-H2AX foci and comet assay confirmed that enhanced RBE is caused by impaired DSB repair. These data offer a novel strategy for enhancing conventional receptor-mediated targeting with an additional, potentially synergistic radiobiological targeting that could be applied to TNBC. Mol Cancer Ther; 12(10); 2043-54. Ó2013 AACR.

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Mitochondrial DNA mutations in respiratory complex-I in never-smoker lung cancer patients contribute to lung cancer progression and associated with EGFR gene mutation

Journal of Cellular Physiology, 2012

Mitochondrial DNA (mtDNA) mutations were reported in different cancers. However, the nature and r... more Mitochondrial DNA (mtDNA) mutations were reported in different cancers. However, the nature and role of mtDNA mutation in never-smoker lung cancer patients including patients with EGFR and KRAS gene mutation are unknown. In the present study, we sequenced entire mitochondrial genome (16.5 kb) in matched normal and tumors obtained from 30 never-smoker and 30 currentsmoker lung cancer patients, and determined the mtDNA content. All the patients' samples were sequenced for KRAS (exon 2) and EGFR (exon 19 and 21) gene mutation. The impact of forced overexpression of a respiratory complex-I gene mutation was evaluated in a lung cancer cell line. We observed significantly higher (P=0.006) mtDNA mutation in the never-smokers compared to the current-smoker lung cancer patients. MtDNA mutation was significantly higher (P=0.026) in the never-smoker Asian compared to the current-smoker Caucasian patients' population. MtDNA mutation was significantly (P=0.007) associated with EGFR gene mutation in the never-smoker patients. We also observed a significant increase (P=0.037) in mtDNA content among the neversmoker lung cancer patients. The majority of the coding mtDNA mutations targeted respiratory complex-I and forced overexpression of one of these mutations resulted in increased in vitro proliferation, invasion and superoxide production in lung cancer cells. We observed a higher prevalence and new relationship between mtDNA alterations among never-smoker lung cancer patients and EGFR gene mutation. Moreover, a representative mutation produced strong growth effects after forced overexpression in lung cancer cells. Signature mtDNA mutations provide a basis to develop novel biomarkers and therapeutic strategies for never-smoker lung cancer patients.

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Molecular biology of adenoid cystic carcinoma

Head & Neck, 2011

Background-Adenoid cystic carcinoma (ACC) is an unusual salivary gland malignancy that remains po... more Background-Adenoid cystic carcinoma (ACC) is an unusual salivary gland malignancy that remains poorly understood. Standard treatment, including surgery with postoperative radiation therapy have attained reasonable local control rates, but the propensity for distant metastases has limited any improvement in survival over time. Our understanding of the molecular mechanisms driving adenoid cystic carcinoma is quite rudimentary, due to the infrequent nature of its occurrence. Methods-An extensive literature review was performed on salivary gland adenoid cystic carcinoma and basic science research findings. Results-This review highlights many findings that are emerging about the carcinogenesis of ACC including cytogenetics, tumor suppressor genes, oncogenes, epigenetic alterations, mitochondrial alterations, and biomarker studies. Conclusions-While there have been many discoveries, much still remains unknown about this rare malignancy.

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Hemimethylation footprints of DNA demethylation in cancer

Epigenetics, 2009

Clusterin Is a Gene-Specific Target of microRNA-21 in Head and Neck Squamous Cell Carcinoma

Clinical Cancer Research, 2013

Training Grant (T32DC000027). Funders had no role in study design, data collection, analysis, dec... more Training Grant (T32DC000027). Funders had no role in study design, data collection, analysis, decision to publish, or preparation of the manuscript. Study was also funded by Asuragen, Inc. The researchers at Asuragen, Inc. who participated in this study were not influenced by management or parties outside of their research group and had exclusive control over study design, data collection, analysis, decision to publish, and preparation of the manuscript.

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BORIS Binding to the Promoters of Cancer Testis Antigens, MAGEA2, MAGEA3, and MAGEA4, Is Associated with Their Transcriptional Activation in Lung Cancer

Clinical Cancer Research, 2011

Purpose: Aim of this study was to determine whether BORIS (Brother of the Regulator of Imprinted ... more Purpose: Aim of this study was to determine whether BORIS (Brother of the Regulator of Imprinted Sites) is a regulator of MAGEA2, MAGEA3, and MAGEA4 genes in lung cancer. Experimental Design: Changes in expression of MAGEA genes upon BORIS induction/knockdown were studied. Recruitment of BORIS and changes in histone modifications at their promoters upon BORIS induction were analyzed. Luciferase assays were used to study their activation by BORIS. Changes in methylation at these promoters upon BORIS induction were evaluated. Results: Alteration of BORIS expression by induction/knockdown directly correlated with expression of MAGEA genes. BORIS was enriched at their promoters in H1299 cells, which show high expression of these cancer testis antigens (CTA), compared with normal human bronchial epithelial (NHBE) cells which show low expression of the target CTAs. BORIS induction in A549 cells resulted in increased amounts of BORIS and activating histone modifications at their promoters along with a corresponding increase in their expression. Similarly, BORIS binding at these promoters in H1299 correlates with enrichment of activating modifications, whereas absence of BORIS binding in NHBE is associated with enrichment of repressive marks. BORIS induction of MAGEA3 was associated with promoter demethylation, but no methylation changes were noted with activation of MAGEA2 and MAGEA4. Conclusions: These data suggest that BORIS positively regulates these CTAs by binding and inducing a shift to a more open chromatin conformation with promoter demethylation for MAGEA3 or independent of promoter demethylation in case of MAGEA2 and MAGEA4 and may be a key effector involved in their derepression in lung cancer. Clin Cancer Res; 17(13); 4267-76. Ó2011 AACR.

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