A post-COVID survey of current and future parents among faculty, trainees, and research staff at an NCI-designated cancer center

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Background: Challenges for women in science and academic medicine have been well documented, which include gender disparities related to parental and domestic responsibilities that interfere with work or career opportunities. We aimed to evaluate the experiences and working environment at an NCI-designated Cancer Center for current and future parents in the post-COVID era. We hypothesized there would be differences in the experiences of parents between men and women, and between trainees, faculty, and staff. Methods: A 61-question online survey for current and future parents was developed by the Women’s Task Force of the Hillman Cancer Center (HCC) in Pittsburgh, Pennsylvania. Questions focused on perceived attitudes towards parents, the supportive nature of the working environment for parents, experiences with breastfeeding as a working parent, and childcare responsibilities pre- and post-COVID. The survey was sent to 562 scientific faculty, physicians, trainees, and research staff at HCC. Comparisons between groups of interest were performed using a chi-square test. Results: There were 214 respondents (38% response rate) with even representation: 38% were faculty, 27% were trainees, and 35% were research staff; 59% were female. 6% of respondents reported being “discouraged or excluded from participating in specific activities due to having or planning children”, and 24% felt “moderately supported” as a parent at work. Regarding breastfeeding, 58% reported that the decision to breastfeed was moderately impacted by returning to work, and of the women who were currently or recently breastfeeding, 42% reported that there were not enough lactation rooms in their building. Other questions in the survey aimed to evaluate what further support would be helpful for parents. 40% reported that on-site childcare would help better support them as a parent, especially because 47% documented that finding childcare was difficult and 53% documented that they looked at ≥4 daycares or nannies. Further, 49% reported that they did not know where to look for resources in finding childcare. Pre-COVID, 32% reported spending 2-3 hours a day on childcare and/or home responsibilities; post-COVID, 55% reported spending ≥4 hours a day. These effects were more pronounced in women compared to men (p < 0.05). Pre-COVID, 40% reported that they were unable to participate in work events due to childcare responsibilities, which increased to 54% post-COVID, and was most pronounced in faculty and trainees compared to staff (p < 0.05). Conclusions: Our survey describes some of the universal challenges of working parents in Oncology, which have been exacerbated by COVID. The impact of COVID was more pronounced in women. Further studies are needed for systematic interventions or policies that improve support for working parents, including unified resources and working groups for current and expecting parents.

Expression of TIM3/VISTA checkpoints and the CD68 macrophage-associated marker correlates with anti-PD1/PDL1 resistance: implications of immunogram heterogeneity

Although immunotherapies have achieved remarkable salutary effects among subgroups of advanced cancers, most patients do not respond. We comprehensively evaluated biomarkers associated with the "cancer-immunity cycle" in the pan-cancer setting in order to understand the immune landscape of metastatic malignancies as well as anti-PD-1/PD-L1 inhibitor resistance mechanisms. Interrogation of 51 markers of the cancer-immunity cycle was performed in 101 patients with diverse malignancies using a clinical-grade RNA sequencing assay. Overall, the immune phenotypes demonstrated overexpression of multiple checkpoints including VISTA (15.8% of 101 patients), PD-L2 (10.9%), TIM3 (9.9%), LAG3 (8.9%), PD-L1 (6.9%) and CTLA4 (3.0%). Additionally, aberrant expression of macrophage-associated markers (e.g. CD68 and CSF1R; 11-23%), metabolic immune escape markers (e.g. ADORA2A and IDO1; 9-16%) and T-cell priming markers (e.g. CD40, GITR, ICOS and OX40; 4-31%) were observed. Most tumors (87.1%, 88/101) expressed distinct immune portfolios, with a median of six theoretically actionable biomarkers (pharmacologically tractable by Food and Drug Administration approved agents [on- or off-label] or with agents in clinical development). Overexpression of TIM-3, VISTA and CD68 were significantly associated with shorter progression-free survival (PFS) after anti-PD-1/PD-L1-based therapies (among 39 treated patients) (all P < .01). In conclusion, cancer-immunity cycle biomarker evaluation was feasible in diverse solid tumors. High expression of alternative checkpoints TIM-3 and VISTA and of the macrophage-associated markers CD68 were associated with significantly worse PFS after anti-PD-1/PD-L1-based therapies. Most patients had distinct and complex immune expression profiles suggesting the need for customized combinations of immunotherapy.

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor (ICI) response in metastatic renal cell carcinoma (mRCC)

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Background: ICIs are now standard of care for mRCC; however, there are few biomarkers to predict ICI response. Recent data from atezolizumab/bevacizumab trials in mRCC suggest tumors with high Teffhigh/PD-L1+ are more likely to respond to ICI. Here, we use two gene panels as well as other inflammation markers in the tumor microenvironment to correlate with ICI responses. Methods: This multicenter study evaluated 86 patients (pts) with mRCC treated with ICIs. FFPE tumor samples were evaluated by RNA sequencing for Teff status. Two gene panels were analyzed: a Teff Gene Panel (CD8, CD27, IFNG, GZMA, GZMB, PRF1, EOMES, CXCL9, CXCL10, CXCL11, CD274, CTLA4, FOXP3, TIGIT, IDO1, PSMB9, TAP1) and a 5-Gene panel (FOXP3, CCR4, KLRK1, ITK, and TIGIT) based on the gene expression pattern of tumors in our cohort. Objective response rates (ORRs, defined as CRs and PRs) were correlated with PD-L1 status (positivity was defined as ≥1% TPS based on Dako 22C3 IHC assay), and TMB (0-10, 10-20, ≥20 mut/Mb), and tumor inflammation (high CD8 expression compared to a large reference population). Best responses to ICI was determined by an expert radiologist using RECIST 1.1 criteria. Inflamed tumor status, Teff gene panel, 5-gene panel, PD-L1 status, and TMB were associated with ORR and tested using a chi-squared test with Yates’s continuity correction. Results: ORR was 50% (4/8) for PD-L1 positive pts and 14% (9/65) for PD-L1 negative pts (p = 0.042). The majority of tumors (95%, 82/86) had TMB < 10 mut/mb. 43 pts (50%) were classified as Teffhigh and 43 pts were classified as Tefflow. ORR was 23% (10/43) in the Teffhigh cohort and 12% (5/43) in the Tefflow cohort (p = 0.256). ORR was 31% (14/45) in the 5-Gene high cohort and 2% (1/41) in the 5-Gene low cohort (p = 0.001). Conclusions: TMB and tumor inflammation based on CD8 did not reliably predict for objective responses in this study of mRCC pts treated with ICIs. Gene expression signatures provide a more comprehensive evaluation of the tumor microenvironment and may lead to better predictive biomarkers for ICI response than individual biomarkers such as PD-L1, TMB, or CD8 expression.

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor (ICI) response in metastatic renal cell carcinoma (mRCC)

63

Background: ICIs are now standard of care for mRCC; however, there are few biomarkers to predict ICI response. Recent data from atezolizumab/bevacizumab trials in mRCC suggest tumors with high Teffhigh/PD-L1+ are more likely to respond to ICI. Here, we use this Teff gene panel as well as other markers of inflammation in the tumor microenvironment to correlate with ICI responses. Methods: This multicenter study evaluated 69 pts with mRCC treated with ICIs. FFPE tumor samples were evaluated by RNA sequencing to measure transcript levels of genes related Teff status. Teff status was defined as the mRNA expression of 17 genes (CD8, CD27, IFNG, GZMA, GZMB, PRF1, EOMES, CXCL9, CXCL10, CXCL11, CD274, CTLA4, FOXP3, TIGIT, IDO1, PSMB9, TAP1), with Teffhigh/low separated at the median. PD-L1 positivity was defined as ≥1% TPS based on Dako 22C3 IHC assay, and TMB high as > 10 mutations per megabase. Inflamed tumors were defined as CD8 expression in the top 75th percentile compared to a large reference population of multiple tumor types. Best responses to ICI was determined by an expert radiologist using RECIST 1.1 criteria. Inflamed tumor status, Teff gene expression, PD-L1 positive, and TMB were associated with disease control (DC, defined as CR, PR, or stable disease). DC comparisons were tested using a chi-squared test with Yates’s continuity correction. Results: DC was 63% (5/8) amongst PD-L1 positive pts and 52% (31/60) in PD-L1 negative patients (p = 0.84). Only 2 pts were TMB high. The majority of mRCC tumors (97%, 67/69) were TMB low. 6-month DC in TMB high tumors was 50% (1/2) and 49.3% (33/67) in TMB low tumors (p = 1.0). 36 pts were classified as Teffhigh and 33 patients were classified as Tefflow. 6-month DC was 61% (22/36) in the Teffhigh cohort and 36% (12/33) in the Tefflow cohort (p = 0.069). 6-month DC was 64% of inflamed tumors (16/25) vs 41% of non-inflamed tumors (18/44) (p = 0.111). Conclusions: TMB high and PD-L1 expression do not reliably predict for DC in pts with mRCC. Utilizing a gene signature score may better predict ICI response.

RNA-sequencing reveals immunotherapy targets in gynecological cancer

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Background: We performed microsatellite instability testing and expression immune profiling of endometrioid and serous carcinomas to identify immunotherapeutic targets and histologic attribute correlates. Methods: Microsatellite instability and RNA-seq of 395 immune-related genes were performed in 37 endometrioid and 53 serous carcinomas. Each gene was ranked against a reference population and subsequently compared to a separate clinical database reference of diverse neoplasms to perform Wilcoxon ranked sum test comparisons. Benjamin-Hochberg corrected p-values are reported. Results: VTCN1, IDO1, LAG3, and components of the mTOR/AKT1 pathway were overexpressed in both endometrioid and serous carcinomas compared to the clinical database population. CD276 and NT5E were uniquely overexpressed in the endometrioid set (Table). In the endometrioid set ADGRE5 was overexpressed in endometrioid primaries when compared to their metastatic counterparts. Serous metastases relatively overexpressed HLA-DPA1 compared to their primary counterparts. Ten of 26 endometrioid cancers with available microsatellite instability status were microsatellite unstable. All serous carcinomas were microsatellite stable. There was no correlation between microsatellite instability status and expression of any gene in either endometrioid or serous cancers. Conclusions: We identified high RNA-expression of VTCN1, IDO1, CD276, and LAG3 in endometrioid and serous carcinomas while NT5E (ADORA2A ligand) was found to be uniquely upregulated in endometrioid carcinomas. These markers may play a role in immune suppression in gynecological cancers and are potential immunotherapeutic targets. The upregulation of ADGRE5 in primary endometrioid cancers and upregulation of HLA-DPA1 in metastatic serous cancers suggests immunologic differences which may be relevant to the formation of metastatic disease.

Evaluation of tumor microenvironment and biomarkers of immune checkpoint inhibitor (ICI) response in metastatic renal cell carcinoma (mRCC)

607

Background: ICIs are now standard of care for mRCC; however, there are few biomarkers to predict ICI response. Recent data from atezolizumab/bevacizumab trials in mRCC suggest tumors with high Teffhigh/PD-L1+ are more likely to respond to ICI. Here, we use this Teff gene panel as well as other markers of inflammation in the tumor microenvironment to correlate with ICI responses. Methods: This multicenter study evaluated 69 pts with mRCC treated with ICIs. FFPE tumor samples were evaluated by RNA sequencing to measure transcript levels of genes related Teff status. Teff status was defined as the mRNA expression of 17 genes (CD8, CD27, IFNG, GZMA, GZMB, PRF1, EOMES, CXCL9, CXCL10, CXCL11, CD274, CTLA4, FOXP3, TIGIT, IDO1, PSMB9, TAP1), with Teffhigh/low separated at the median. PD-L1 positivity was defined as ≥1% TPS based on Dako 22C3 IHC assay, and TMB high as > 10 mutations per megabase. Inflamed tumors were defined as CD8 expression in the top 75th percentile compared to a large reference population of multiple tumor types. Best responses to ICI was determined by an expert radiologist using RECIST 1.1 criteria. Inflamed tumor status, Teff gene expression, PD-L1 positive, and TMB were associated with disease control (DC, defined as CR, PR, or stable disease). DC comparisons were tested using a chi-squared test with Yates’s continuity correction. Results: DC was 63% (5/8) amongst PD-L1 positive pts and 52% (31/60) in PD-L1 negative patients (p = 0.84). Only 2 pts were TMB high. The majority of mRCC tumors (97%, 67/69) were TMB low. 6-month DC in TMB high tumors was 50% (1/2) and 49.3% (33/67) in TMB low tumors (p = 1.0). 36 pts were classified as Teffhigh and 33 patients were classified as Tefflow. 6-month DC was 61% (22/36) in the Teffhigh cohort and 36% (12/33) in the Tefflow cohort (p = 0.069). 6-month DC was 64% of inflamed tumors (16/25) vs 41% of non-inflamed tumors (18/44) (p = 0.111). Conclusions: TMB high and PD-L1 expression do not reliably predict for DC in pts with mRCC. Utilizing a gene signature score may better predict ICI response.

Predicting response to checkpoint inhibitors in melanoma beyond PD-L1 and mutational burden

BACKGROUND

Immune checkpoint inhibitors (ICIs) have changed the clinical management of melanoma. However, not all patients respond, and current biomarkers including PD-L1 and mutational burden show incomplete predictive performance. The clinical validity and utility of complex biomarkers have not been studied in melanoma.

METHODS

Cutaneous metastatic melanoma patients at eight institutions were evaluated for PD-L1 expression, CD8+ T-cell infiltration pattern, mutational burden, and 394 immune transcript expression. PD-L1 IHC and mutational burden were assessed for association with overall survival (OS) in 94 patients treated prior to ICI approval by the FDA (historical-controls), and in 137 patients treated with ICIs. Unsupervised analysis revealed distinct immune-clusters with separate response rates. This comprehensive immune profiling data were then integrated to generate a continuous Response Score (RS) based upon response criteria (RECIST v.1.1). RS was developed using a single institution training cohort (n = 48) and subsequently tested in a separate eight institution validation cohort (n = 29) to mimic a real-world clinical scenario.

RESULTS

PD-L1 positivity ≥1% correlated with response and OS in ICI-treated patients, but demonstrated limited predictive performance. High mutational burden was associated with response in ICI-treated patients, but not with OS. Comprehensive immune profiling using RS demonstrated higher sensitivity (72.2%) compared to PD-L1 IHC (34.25%) and tumor mutational burden (32.5%), but with similar specificity.

CONCLUSIONS

In this study, the response score derived from comprehensive immune profiling in a limited melanoma cohort showed improved predictive performance as compared to PD-L1 IHC and tumor mutational burden.

Abstract 4215: Rapid, inexpensive and accurate detection of rare variants by targeted sequencing

Next generation sequencing technology is quickly becoming the most rapid and accurate method of determining mutation profiles of patient's tumor samples. While whole genome or exome sequencing profiles are the most comprehensive methods for complete exploration of these tumors, these protocols typically require large amounts of DNA, are expensive, don't get deep coverage, and require extensive time for library and sample preparation. Ion Torrent has developed new methodology for looking at 10’s to 1000’s of genomic targets with the Ion AmpliSeq™ technology. The recommended input of 10ng of DNA is suitable for work with FFPE or fine needle biopsy samples, and has been demonstrated on samples with less than 1ng of DNA. In a 10 hour day this protocol can take isolated DNA through the library and sample prep as well sequencing with variant calls, making it an incredibly rapid method for determining sequence variants within targeted regions. There are currently two commercially available cancer-specific amplicon panels: the Comprehensive Cancer Panel (CCP) uses ∼16,000 primer pairs covering the exons of 409 tumor suppressor genes and oncogenes frequently cited and mutated in cancers, and the Cancer Hotspot Panel v2 (CHP2) uses 207 primer pairs in 50 clinically actionable genes to detect over 2800 mutation hotspots. We recently measured the sensitivity of SNP detection levels with the CCP and CHP2 panels on a 90:10 (reference:SNP) admixed sample and were able to detect SNP proportions of 2.0%(p&lt;0.005) with CHP2 and 2.0% (p&lt;0.001) with CCP. The CHP2 amplicons yielded coverages of &gt;2000X for a single sample on a 314 chip and &gt;3000X for 6 barcoded samples on a 318 chip. Comparatively, the average base coverage of the CCP was &gt;280x and over 95% of the CCP amplicons were covered at &gt;50X. We ran the CCP in quadruplicate on 318 chips at two separate facilities and the CHP2 was run barcoded on 318 chips and single samples on 314 chips also in quadruplicate at two separate facilities and all of the chips show very equivalent numbers for SNP detection and coverages. These results demonstrate the consistent nature of targeted sequencing using a next gen platform. Going from isolated DNA to variant calling in as little as 10 hrs, this method is extremely fast and efficient which will be critical in future diagnostic settings.

Citation Format: Devin Dressman, Stefanie Nishimura, Charles Scafe, Yutao Fu, Ellen Fanti, Lev Kotler, Vaish Panchapakesa, Wendell Orphe, Sherry Hansen, Nick Hapshe, Carl Fergus, Erin Lagier, Eric Wei, Grace Lui, Reddy Nallapareddy, Xiaohui Chen, Zhitong Liu, Eugeni Namsaraev. Rapid, inexpensive and accurate detection of rare variants by targeted sequencing. [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 4215. doi:10.1158/1538-7445.AM2013-4215

X-linked infantile spinal muscular atrophy: clinical definition and molecular mapping

PURPOSE

X-linked infantile spinal-muscular atrophy (XL-SMA) is a rare disorder, which presents with the clinical characteristics of hypotonia, areflexia, and multiple congenital contractures (arthrogryposis) associated with loss of anterior horn cells and death in infancy. We have previously reported a single family with XL-SMA that mapped to Xp11.3-q11.2. Here we report further clinical description of XL-SMA plus an additional seven unrelated (XL-SMA) families from North America and Europe that show linkage data consistent with the same region.

METHODS

We first investigated linkage to the candidate disease gene region using microsatellite repeat markers. We further saturated the candidate disease gene region using polymorphic microsatellite repeat markers and single nucleotide polymorphisms in an effort to narrow the critical region. Two-point and multipoint linkage analysis was performed using the Allegro software package.

RESULTS

Linkage analysis of all XL-SMA families displayed linkage consistent with the original XL-SMA region.

CONCLUSION

The addition of new families and new markers has narrowed the disease gene interval for a XL-SMA locus between SNP FLJ22843 near marker DXS 8080 and SNP ARHGEF9 which is near DXS7132 (Xp11.3-Xq11.1).

BEAMing up for detection and quantification of rare sequence variants

BEAMing allows the one-to-one conversion of a population of DNA fragments into a population of beads. We used rolling circle amplification to increase the number of copies bound to such beads by more than 100-fold. This allowed enumeration of mutant and wild-type sequences even when they were present at ratios less than 1:10,000 and was sensitive enough to directly quantify the error rate of DNA polymerases used for PCR.

Detection and quantification of mutations in the plasma of patients with colorectal tumors

The early detection of cancers through analysis of circulating DNA could have a substantial impact on morbidity and mortality. To achieve this goal, it is essential to determine the number of mutant molecules present in the circulation of cancer patients and to develop methods that are sufficiently sensitive to detect these mutations. Using a modified version of a recently developed assay for this purpose, we found that patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli (APC) DNA molecules in their plasma. The median number of APC DNA fragments in such patients was 47,800 per ml of plasma, of which 8% were mutant. Mutant APC molecules were also detected in >60% of patients with early, presumably curable colorectal cancers, at levels ranging from 0.01% to 1.7% of the total APC molecules. These results have implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.

Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations

Many areas of biomedical research depend on the analysis of uncommon variations in individual genes or transcripts. Here we describe a method that can quantify such variation at a scale and ease heretofore unattainable. Each DNA molecule in a collection of such molecules is converted into a single magnetic particle to which thousands of copies of DNA identical in sequence to the original are bound. This population of beads then corresponds to a one-to-one representation of the starting DNA molecules. Variation within the original population of DNA molecules can then be simply assessed by counting fluorescently labeled particles via flow cytometry. This approach is called BEAMing on the basis of four of its principal components (beads, emulsion, amplification, and magnetics). Millions of individual DNA molecules can be assessed in this fashion with standard laboratory equipment. Moreover, specific variants can be isolated by flow sorting and used for further experimentation. BEAMing can be used for the identification and quantification of rare mutations as well as to study variations in gene sequences or transcripts in specific populations or tissues.

Overexpression of the EGFR/FKBP12/HIF-2alpha pathway identified in childhood astrocytomas by angiogenesis gene profiling

Intense angiogenesis proliferation, a histopathological hallmark distinguishing malignant from benign astrocytoma, is vital for tumor progression. Thus, identifying and targeting specific pathways that promote malignant astrocytoma-induced angiogenesis could have substantial therapeutic benefit. Expression profiling of 13 childhood astrocytomas to determine the expression pattern of 133 angiogenesis-related genes revealed that 44 (33%) genes were differentially expressed (17 were overexpressed, and 27 were underexpressed) between malignant high-grade astrocytomas (HGAs) and benign low-grade astrocytomas. Hierarchical clustering and principal components analysis using only the 133 angiogenesis-related genes distinguished HGA from low-grade astrocytoma in 100% of the samples analyzed, as did unsupervised analyses using the entire set of 9198 expressed genes represented on the array, indicating that the angiogenesis-related genes were reliable markers of pathological grade. A striking new finding was significant overexpression of hypoxia-inducible transcription factor (HIF)-2alpha as well as high-level expression of FK506-binding protein (FKBP) 12 by HGA. Furthermore, 9 of 21 (43%) genes overexpressed by HGA were HIF/FKBP-associated genes. This group included the epidermal growth factor receptor (EGFR), which promotes HIF synthesis, as well as insulin-like growth factor-binding protein 2 (IGFBP2), a target gene of HIF activity. Differential protein expression of HIF-2alpha was validated in an independent group of 16 astrocytomas (P = 0.02). We conclude that the EGFR/FKBP12/HIF-2alpha pathway is important in childhood HGA and represents a potential new therapeutic target.

Delivery of alpha- and beta-sarcoglycan by recombinant adeno-associated virus: efficient rescue of muscle, but differential toxicity

The sarcoglycanopathies are a group of four autosomal recessive limb girdle muscular dystrophies (LGMD 2D, 2E, 2C, and 2F), caused by mutations of the alpha-, beta-, gamma-, or delta-sarcoglycan genes, respectively. The delta-sarcoglycan-deficient hamster has been the most utilized model for gene delivery to muscle by recombinant adeno-associated virus (AAV) vectors; however, human patients with delta-sarcoglycan deficiency are exceedingly rare, with only two patients described in the United States. Here, we report construction and use of AAV vectors expressing either alpha- or beta-sarcoglycan, the genes responsible for the most common forms of the human sarcoglycanopathies. Both vectors showed successful short-term genetic, biochemical, and histological rescue of both alpha- and beta-sarcoglycan-deficient mouse muscle. However, comparison of persistence of expression in 51 injected mice showed substantial differences between AAV alpha-sarcoglycan (alpha-SG) and beta-sarcoglycan (beta-SG) vectors. AAV-beta-SG showed long-term expression with no decrease in expression for more than 21 months after injection, whereas AAV-alpha-SG showed a dramatic loss of positive fibers between 28 and 41 days post-injection (p = 0.006). Loss of immunopositive myofibers was correlated with significant inflammatory cell infiltrate, primarily macrophages. To determine whether the loss of alpha-sarcoglycan-positive fibers was due to an immune response or cytotoxic effect of alpha-sarcoglycan overexpression, severe combined immunodeficient (SCID) mouse muscle was assayed for cytotoxicity after injection with AAV-alpha-SG, AAV-beta-SG, or phosphate-buffered saline. The results were consistent with overexpression of alpha-sarcoglycan causing significant cytotoxicity. The cytotoxicity of alpha-sarcoglycan, and not beta- or delta-sarcoglycan overexpression, was consistent with biochemical studies of the hierarchical order of assembly of the sarcoglycan complex. Our data suggest that even closely related proteins might require different levels of expression to avoid toxicity and achieve long-term tissue rescue.

Slug is a novel downstream target of MyoD. Temporal profiling in muscle regeneration

Temporal expression profiling was utilized to define transcriptional regulatory pathways in vivo in a mouse muscle regeneration model. Potential downstream targets of MyoD were identified by temporal expression, promoter data base mining, and gel shift assays; Slug and calpain 6 were identified as novel MyoD targets. Slug, a member of the snail/slug family of zinc finger transcriptional repressors critical for mesoderm/ectoderm development, was further shown to be a downstream target by using promoter/reporter constructs and demonstration of defective muscle regeneration in Slug null mice.

Molecular pathophysiology and targeted therapeutics for muscular dystrophy

Experimental therapeutics of the muscular dystrophies has made impressive advances on several fronts. Adeno-associated virus has emerged as the clear 'vector of choice' for muscle gene delivery, with successful functional rescue of dystrophic muscle in rodent models. Correction of the dystrophin gene mutation in a dog model has been reported, and several reports of progress on myogenic stem cell characterization are resurrecting cell transplantation as a possible therapeutic approach. The downstream consequences of dystrophin deficiency are being defined quickly using microarray experiments, and drugs targeting specific biochemical pathways are being tested rapidly in animal models. Such targeted drug discoveries, which are discussed in this article, have begun to be implemented in human clinical trials.

RNA differential display of scarless wound healing in fetal rabbit indicates downregulation of a CCT chaperonin subunit and upregulation of a glycophorin-like gene transcript

BACKGROUND/PURPOSE

Scars form as wounds heal in adult organisms. In addition to disrupting cosmetic appearance, scar tissue can cause significant morbidity, and even death if it blocks vital organ function. Previous work has established that fetal wounds, especially in early to midgestation, can heal without scarring. Because such inherent physiological mechanisms ultimately are under genetic control, a study was initiated to elucidate the differences in gene expression that produce scarless wound healing in the mammalian fetus but scarring in postnatal wounds. Reverse transcription polymerase chain reaction (RT-PCR) differential display (DD) was used to detect differentially expressed mRNA transcripts in a rabbit model of wound healing.

METHODS

Adult and 21-day fetal full-thickness rabbit skin specimens from wounded and unwounded sites were harvested 12 hours postwounding. RNA extracted from the tissue was used as a template in DD reactions using anchoring and random primers to generate tissue-specific gene expression fingerprints. The over 2,000 resulting amplimers (gene transcripts) were screened for differential expression among the 4 types of specimens: fetal control (unwounded), fetal wound, adult control, and adult wound. Selected bands distinctly upregulated or downregulated in fetal wound lanes on the DD gels were excised, and the cDNA was extracted, reamplified, cloned into vectors, and sequenced. DD results were confirmed by limiting-dilution RT-PCR using sequence-specific primers.

RESULTS

Differential display (DD) showed 22 amplimers that were significantly upregulated in all fetal wound samples as compared with little or no expression in fetal control, adult control, or adult wound tissues. Conversely, 5 transcripts were downregulated in the fetal wound specimens but highly expressed in the 3 comparison tissues. Reamplification of selected transcripts by PCR, followed by cloning and DNA sequencing, yielded 7 distinct sequences, each representing a gene expressed differently in fetal wound than in the other 3 tissues. A transcript that was downregulated in fetal wound showed very high sequence homology to part of the human gene for the eta subunit of the hetero-oligomeric particle CCT (the chaperonin containing T-complex polypeptide 1 or TCP-1). An upregulated amplimer showed significant DNA sequence homology to glycophorins A and B. One sequence was identified as 28S rRNA. The remaining 4 candidate sequences showed no significant homology to known genes, but 1 had high homology to expressed sequence tags of unknown function.

CONCLUSIONS

With careful experimental design and proper controls and verifications, differential display of RNA expression is a potentially powerful method of finding genes that specifically regulate a particular physiological process such as fetal wound healing. No a priori knowledge of what genes might be involved, or why, is necessary. This study indicates that downregulation of a gene that codes for a chaperonin subunit and upregulation of several other genes may be involved in the striking scarless character of wound healing in the mammalian fetus. Results suggest the hypothesis that downregulation of the CCT chaperonin in fetal wound may inhibit the formation of myofibroblasts, a cell type that correlates highly with scarring in postnatal wound healing, by preventing the folding of sufficient alpha-smooth muscle actin to form the stress fibers characteristic of these cells.

Full functional rescue of a complete muscle (TA) in dystrophic hamsters by adeno-associated virus vector-directed gene therapy

Limb girdle muscular dystrophy (LGMD) 2F is caused by mutations in the delta-sarcoglycan (SG) gene. Previously, we have shown successful application of a recombinant adeno-associated virus (AAV) vector for genetic and biochemical rescue in the Bio14.6 hamster, a homologous animal model for LGMD 2F (J. Li et al., Gene Ther. 6:74-82, 1999). In this report, we show efficient and long-term delta-SG expression accompanied by nearly complete recovery of physiological function deficits after a single-dose AAV vector injection into the tibialis anterior muscle of the dystrophic hamsters. AAV vector treatment led to more than 97% recovery in muscle strength for both the specific twitch force and the specific tetanic force, when compared to the age-matched control. Vector treatment also prevented pathological muscle hypertrophy and resulted in normal muscle weight and size. Finally, vector-treated muscle showed substantial improvement of the histopathology. This is the first report of successful functional rescue of an entire muscle after AAV-mediated gene delivery. This report also demonstrates the feasibility of in vivo gene therapy for LGMD patients by using AAV vectors.

rAAV vector-mediated sarcogylcan gene transfer in a hamster model for limb girdle muscular dystrophy

The limb girdle muscular dystrophies (LGMD) are a genetically and phenotypically heterogeneous group of degenerative neuromuscular diseases. A subset of the genetically recessive forms of LGMD are caused by mutations in the four muscle sarcoglycan genes (alpha, beta, gamma and delta). The coding sequences of all known sarcoglycan genes are smaller than 2 kb, and thus can be readily packaged in recombinant adeno-associated virus (rAAV) vectors. Previously, we have demonstrated highly efficient and sustained transduction in mature muscle tissue of immunocompetent animals with rAAV vectors. In this report, we utilize recombinant AAV containing the delta-sarcoglycan gene for genetic complementation of muscle diseases using a delta-sarcoglycan-deficient hamster model (Bio 14.6). We show efficient delivery and widespread expression of delta-sarcoglycan after a single intramuscular injection. Importantly, rAAV vector containing the human delta-sarcoglycan cDNA restored secondary biochemical deficiencies, with correct localization of other sarcoglycan proteins to the muscle fiber membrane. Interestingly, restoration of alpha-, as well as beta-sarcoglycan was homogeneous and properly localized throughout transduced muscle, and appeared unaffected by dramatic overexpression of delta-sarcoglycan in the cytoplasm of some myofibers. These results support the feasibility of rAAV vector's application to treat LGMD by means of direct in vivo gene transfer.