An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue

MALDI MS imaging (MSI) is a powerful analytical tool for spatial peptide detection in heterogeneous tissues. Proper sample preparation is crucial to achieve high quality, reproducible measurements. Here we developed an optimized protocol for spatially resolved proteolytic peptide detection with MALDI time‐of‐flight MSI of fresh frozen prostate tissue sections. The parameters tested included four different tissue washes, four methods of protein denaturation, four methods of trypsin digestion (different trypsin densities, sprayers, and incubation times), and five matrix deposition methods (different sprayers, settings, and matrix concentrations). Evaluation criteria were the number of detected and excluded peaks, percentage of high mass peaks, signal‐to‐noise ratio, spatial localization, and average intensities of identified peptides, all of which were integrated into a weighted quality evaluation scoring system. Based on these scores, the optimized protocol included an ice‐cold EtOH+H₂O wash, a 5 min heating step at 95°C, tryptic digestion incubated for 17h at 37°C and CHCA matrix deposited at a final amount of 1.8 μg/mm². Including a heat‐induced protein denaturation step after tissue wash is a new methodological approach that could be useful also for other tissue types. This optimized protocol for spatial peptide detection using MALDI MSI facilitates future biomarker discovery in prostate cancer and may be useful in studies of other tissue types.

Adjunct diagnostic strategies in improving diagnostic yields in image-guided biopsies of musculoskeletal neoplasms-A cost-effectiveness analysis

BACKGROUND

Routine use of adjunct intraprocedural fresh frozen biopsy (FFP) or point-of-care (POC) cytology at the time of image-guided biopsy can improve diagnostic tissue yields for musculoskeletal neoplasms, but these are associated with increased costs.

OBJECTIVE

This study aimed to ascertain the most cost-effective adjunctive test for image-guided biopsies of musculoskeletal neoplasms.

METHODS

This expected value cost-effectiveness microsimulation compared the payoffs of cost (2020 United States dollars) and effectiveness (quality-adjusted life, in days) on each of the competing strategies. A literature review and institutional data were used to ascertain probabilities, diagnostic yields, utility values, and direct medical costs associated with each strategy. Payer and societal perspectives are presented. One- and two-way sensitivity analyses evaluated model uncertainties.

RESULTS

The total cost and effectiveness for each of the strategies were $1248.98, $1414.09, $1980.53, and 80.31, 79.74, 79.69 days for the use of FFP, permanent pathology only, and POC cytology, respectively. The use of FFP dominated the competing strategies. Sensitivity analyses revealed FFP as the most cost-effective across all clinically plausible values.

CONCLUSIONS

Adjunct FFP is most cost-effective in improving the diagnostic yield of image-guided biopsies for musculoskeletal neoplasms. These findings are robust to sensitivity analyses using clinically plausible probabilities.

Morphometry and Contents of the Suprascapular Notch with Potential Clinical Implications: Α Cadaveric Study

Background  The suprascapular notch (SN) represents the point along the route of the suprascapular nerve (SSN) with the greatest potential risk for injury and compression. Thus, factors reducing the area of the notch have been postulated for suprascapular neuropathy development.

Methods  Thirty-one fresh-frozen shoulders were dissected. The contents of the SN were described according to four types as classified by Polguj et al and the middle-transverse diameter of the notch was measured. Also, the presence of an ossified superior transverse scapular ligament (STSL) was identified.

Results  The ligament was partially ossified in 8 specimens (25.8%), fully ossified in 6 (19.35%), and not ossified in the remaining 17 (54.85%). The mean middle-transverse diameter of the SN was 9.06 mm (standard deviation [SD] = 3.45). The corresponding for type-I notches was 8.64 mm (SD = 3.34), 8.86 mm (SD = 3.12) was for type-II, and 14.5 mm (SD = 1.02) was for type III. Middle-transverse diameter was shorter when an ossified ligament was present (mean = 5.10 mm, SD = 0.88 mm), comparing with a partially ossified ligament (mean =7.67 mm, SD = 2.24 mm) and a nonossified one (mean = 11.12 mm, SD = 2.92 mm). No statistically significant evidence was found that the middle-transverse diameter depends on the number of the elements, passing below the STSL.

Conclusion  Our results suggest that SSN compression could be more likely to occur when both suprascapular vessels pass through the notch. Compression of the nerve may also occur when an ossified transverse scapular ligament is present, resulting to significant reduction of the notch's area.

RNA based individualized drug selection in breast cancer patients without patient-matched normal tissue

Background

While standard RNA expression tests stratify patients into risk groups, RNA-Seq can guide personalized drug selection based on expressed mutations, fusion genes, and differential expression (DE) between tumor and normal tissue. However, patient-matched normal tissue may be unavailable. Additionally, biological variability in normal tissue and technological biases may confound results. Therefore, we present normal expression reference data for two sequencing methods that are suitable for breast biopsies.

Results

We identified breast cancer related and drug related genes that are expressed uniformly across our normal samples. Large subsets of these genes are identical for formalin fixed paraffin embedded samples and fresh frozen samples. Adipocyte signatures were detected in frozen compared to formalin samples, prepared by surgeons and pathologists, respectively. Gene expression confounded by adipocytes was identified using fat tissue samples. Finally, immune repertoire statistics were obtained for healthy breast, tumor and fat tissues.

Conclusions

Our reference data can be used with patient tumor samples that are asservated and sequenced with a matching aforementioned method. Coefficients of variation are given for normal gene expression. Thus, potential drug selection can be based on confidently overexpressed genes and immune repertoire statistics.

Materials and Methods

Normal expression from formalin and frozen healthy breast tissue samples using Roche Kapa RiboErase (total RNA) (19 formalin, 9 frozen) and Illumina TruSeq RNA Access (targeted RNA-Seq, aka TruSeq RNA Exome) (11 formalin, 1 frozen), and fat tissue (6 frozen Access). Tumor DE using 10 formalin total RNA tumor samples and 1 frozen targeted RNA tumor sample.

Cryopreservation versus fresh frozen meniscal allograft: A biomechanical comparative analysis

Meniscal allograft transplantation may be a better alternative for the treatment of irreparable meniscal injury compared to other forms of treatment. However, it remains to be seen whether the use fresh frozen allograft is better than cryopreserved allograft in treating this type of injury. We hypothesized that cryopreserved meniscal allograft would work better in maintaining the original biomechanical properties compared to fresh frozen ones, due to the lower amount of damage it incurs during the storage process. We examined young and healthy human menisci obtained from orthopedic oncology patients who underwent resection surgeries around the knee. The menisci obtained were preserved via cryopreservation and deep-freezing process. Traction tests were carried out on the menisci after 6 weeks of preservation. Twelve pairs ( N = 24) of menisci were divided equally into two groups, cryopreservation and deep frozen. There were six males and six female menisci donors for this study. The age range was between 15 and 35 years old (24.9 ± 8.6 years). Cryopreserved specimens had a higher ultimate tensile strength (UTS; 8.2 ± 1.3 Mpa vs. 13.3 ± 1.7 Mpa: p < 0.05) and elastic modulus (61.7 ± 27.6 Mpa vs. 87.0 ± 44.10 Mpa: p < 0.05) compared to the fresh frozen specimens. There was a significant difference in UTS ( p < 0.05) between the two groups but no significant difference in their elastic modulus ( p > 0.05). The elastic modulus of the preserved meniscus was similar to fresh normal menisci taken from other studies (60-120 Mpa; cryopreserved (87.0 ± 44.1) and fresh frozen (61.7 ± 27.5)). Cryopreserved menisci had a higher elastic modulus and point of rupture (UTS) compared to fresh frozen menisci. Cryopreservation proved to be a significantly better method of preservation, among the two methods of preservation in this study.