Citations

ABSTRACTCavin‐4 was identified as a potential autoantigen for immune‐mediated rippling muscle disease (iRMD). To validate this, we developed and tested various immunoassays, including a cell‐based assay (CBA), cavin‐4 recombinant protein ELISA, and multi‐peptide ELISA. Among 19 iRMD patients, all exhibited muscle rippling, and 13 had percussion‐induced mounding. All immunoassays demonstrated clinical and analytical specificities greater than 95%. The protein ELISA had the highest sensitivity (94.7%) and specificity (99.9%), outperforming CBA (sensitivity 89.5%, specificity 99.6%) and the multi‐peptide ELISA (sensitivity 79.0%, specificity 97.2%). Our results suggest that the cavin‐4 protein ELISA is a promising tool for high‐throughput clinical testing in iRMD.

Using 32 immune cell surface markers, we identified 23 monocyte clusters in murine blood. Diabetic gastroparesis was associated with a significant decrease in two circulating classical monocyte-like clusters and an upregulation of the Ccr2-Ccl2 axis in the gastric muscularis propria, suggesting increased tissue monocyte migration. This study offers new targets by pointing to a possible role for two classical monocyte subsets connected to the Ccr2- Ccl2 axis.

Abstract Background While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples for monitoring biomarker discovery, including anatomical location and post-surgical changes, remains unknown. Methods Aptamer-based proteomics was performed on 147 CSF samples from 74 patients; 71 of whom had grade 2–4 astrocytomas or grade 2–3 oligodendrogliomas. This included pre- versus post-resection intracranial CSF samples obtained at early (1–16 days; n = 20 patients) or delayed (86–153 days; n = 11 patients) time points for patients with glioma. Paired lumbar versus intracranial glioma CSF samples were also obtained (n = 14 patients). Results Significant differences were identified in the CSF proteome between lumbar, subarachnoid, and ventricular CSF in patients with gliomas. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome, with distinct sets of proteins present at different time points since resection. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies, such as bevacizumab and immunotherapies. Conclusions The intracranial glioma CSF proteome serves as a rich and dynamic reservoir of potential biomarkers that can be used to evaluate the effects of resection and other therapies over time. All data within this study, including detailed individual clinical annotations, are shared as a resource for the neuro-oncology community to collectively address these unanswered questions and further understand glioma biology through CSF proteomics.

Abstract Adult primary leptomeningeal gliomatosis (PLG) is a rare, rapidly progressive and fatal disease characterized by prominent leptomeningeal infiltration by a glial tumor without an identifiable parenchymal mass. The molecular profile of adult PLG has not been well‐characterized. We report the clinical, pathological, and molecular findings of six adult PLG patients (five males and one female), median age 58 years. All cases exhibited pathological leptomeningeal enhancement at presentation. Leptomeningeal biopsy was diagnostic in five (of six) cases, revealing infiltration by an astrocytic glioma with mitotic activity, lacking microvascular proliferation or necrosis. One case was diagnosed at autopsy. All tumors were IDH‐wildtype, with five harboring TERT promoter mutations. Additional mutations identified were PTEN in one case, TP53 in two cases, and NF1 in two cases. A chromosome profile with +7/−10 was found in four cases, whereas the remaining two showed either chromosome 7 or 7p gain only. Four cases showed chromosome 9p loss with CDKN2A/B homozygous deletion, one case showed hemizygous CDKN2A/B loss, and one case showed intact chromosome 9 and CDK4/GLI1 amplification. DNA methylation profiling was performed in four cases and revealed a match to glioblastoma (GBM) family and mesenchymal typical class with high confidence scores in two cases; the other two cases showed only suggestive combined scores for GBM family and mesenchymal atypical class. The molecular profile of all cases closely aligned with that of adult‐type GBM, IDH‐wildtype, CNS WHO grade 4. All patients succumbed to the disease. In five cases with extensive leptomeningeal disease at diagnosis, the course was rapid, with median survival of 24 days following palliative care. Only one case, with relatively localized disease at diagnosis, received chemoradiation therapy and survived 535 days, raising the possibility that early diagnosis and timely treatment could improve outcome. A detailed list of previously reported cases is provided in a supplementary table.

Background: Beside fibril-forming proteins, amyloid deposits contain other proteins which can influence organ toxicity, disease initiation and clearance. We investigated the association between the amyloid plaque proteomic signature of diagnostic renal biopsies from patients achieving deep and sustained hematologic remissions and renal organ response in AL amyloidosis. Methods: Retrospective study of newly diagnosed AL amyloidosis patients between 2010-2020. Patients were eligible if; (1) they had a baseline renal biopsy which had undergone laser micro-dissection and mass spectrometry, (2) were assessable for renal response [RenR, non-selective proteinuria ≥1g /24 hours, predominantly albumin], (3) were not on renal replacement therapy and did not experience renal progression within 3-months of diagnosis and (4) had RenR measurements, at least twice annually in the first year from treatment and annually thereafter. Patients who did not obtain a renal complete response (RenCR) required a hematologic very good partial response (VGPR) or better within 6 months of treatment initiation, sustained for a minimum of 6 months. Hematological and renal responses were graded according to consensus criteria. Overrepresentation analyses of differentially expressed proteins were performed using the WebGestalt 2019 and the reactome pathway database. A false detection rate corrected p value <0.05 was used to identify significantly overrepresented proteins and pathways. Results: We defined two organ response categories, to capture the extreme ends of the spectrum: renal suboptimal responders (n=24), patients for whom the best renal response was ≤partial response (RenPR), and renal complete responders (n=29), patients who obtained a RenCR at best response. Overall, the median follow-up was 6.7 years (IQR: 5.4-9.2), 6.6 years (IQR: 5.4-8.1) for complete responders, and 8.4 years (IQR: 6.1-11.3) for suboptimal responders. Between renal suboptimal responders and complete responders there was no significant difference in median age (63 vs 63 years, p=0.7), lambda light chain isotype (66% vs 79%, p=0.3), first-line therapy received and renal stage (Stage III: 14% vs 8%, p=0.9). The median time to RenCR was 52-months (IQR: 31-63). Protein pathways over-represented in renal complete responders included 14-3-3 proteins (YWHAG, YWHAH, YWHAQ, YWHAZ), early components of the complement cascade and complement regulatory proteins (C3, C4A, C4B, C8A, complement factor H), keratins, cytoskeletal proteins (tubulin, actin, filamen) and collagen IV. Protein pathways over-represented in renal suboptimal responders included terminal/effector components of the complement cascade (C5, C6, C8B, C9), amyloid signature proteins (ApoA1 and E, vitronectin, clusterin), proteoglycans (heparan sulfate proteoglycan), transgelin and metallopeptidase inhibitor 3. Proteins with the highest-fold increase in renal complete responders included serine protease inhibitor (SERPINA3) and F-box and leucine rich repeat protein (FBXL6), 9.0 x 106 & 7.7-fold, respectively. Proteins with the highest-fold increase in renal suboptimal responders included complement 6 and 8B, 3.5 & 3.6-fold, respectively. Conclusion: This is the first study to identify proteomic determinants of organ response in AL amyloidosis. Molecular chaperones involved in protein aggregate homeostasis, such as the 14-3-3 proteins are upregulated in renal complete responders, similar to what we have shown in our prior work. This suggests that organ responders may have a more favorable microenvironment which “primes” them for organ response after the amyloidogenic light chain has been cleared from the circulation. Renal suboptimal responders (≤RenPR) have elevated levels of terminal complement proteins including membrane attack complex proteins and reduced levels of early components or complement regulatory proteins, which may be responsible for reno-toxic and reno-protective effects, respectively.

Background: Multiple myeloma (MM) involves the proliferation of monoclonal plasma cells (PCs) in the bone marrow. The plasma cell labeling index (PCLI), indicating the percentage of PCs in the S-phase, is a key prognostic factor in newly diagnosed multiple myeloma (NDMM) patients. Methods: A retrospective study at Mayo Clinic analyzed bone marrow Affymetrix microarray datasets from 136 NDMM patients (2001-2012). Data normalization and quality assessment were followed by differential gene expression analysis using limma-voom, adjusted for age, BMPC percentage, and disease stage (RISS). Selected genes were dichotomized by median and subjected to logistic regression for high/low PCLI. Data from 594 patients with a Proliferation Index at baseline was pooled from the MMRF (CoMMpass) dataset for validation after normalization across assays. Results: The baseline characteristics of the patients are as follows: 62 (46%) were female and 74 (54%) were male, with a mean age at diagnosis of 61.6 ± 11.5 years. RISS staging included 36 patients (26.5%) at stage 1, 32 (23.5%) at stage 2, 29 (21.32%) at stage 3, and 39 patients (28.67%) with unknown stage. PCLI distribution showed 113 patients (83.7%) with <2%, and 23 (16.3%) ≥2%. Differential Analysis: The differential analyses reveal several critical insights. In the primary continuous differential analysis, 21,367 genes were analyzed, identifying 654 as differentially expressed with an FDR-adjusted p-value ≤0.05. Of these, 481 genes were upregulated (top 5: SPC25, TRAT1, PBK, E2F8, ASPM) and 173 were downregulated (top 5: SPARC, CD24, MYOF, CXCL12, VCAM1). Univariate and multivariate stratified analyses showed significant findings: 668 genes in age stratification, 395 genes in BMPC% stratification, and 536 genes in RISS stratification. In multivariate analysis, 408 genes were significant with an FDR-adjusted p-value <0.05 for PCLI and ≥0.05 for BMPC%, age, and RISS. 3-Fold Internal Validation: 240 significant genes were identified in fold 1, 25 in fold 2, and 167 in fold 3, with 21 genes common across all folds (e.g., MCM10, GTSE1, UBE2S, NCAPG, FOXM1, STMN1, NEK2, CENPF, MND1, HJURP, E2F8, TOP2A, SKA1, CCNB2, CCNF, CHAF1A, PBK, EXO1, AURKB, CDCA2, DHFR). 19 genes were common in the sensitivity analysis by excluding RISS 3. 20 genes were common in categorical analysis (Categories <1%, 1-2%, 2-3%, 3-4%, >4%). 3 Gene-Based Proliferation Score (3GPS): On univariate logistic regression analysis of 21 genes for high/low PCLI, 17 significant genes were identified. In the step-wise multivariate analysis, CDCA2 (OR=11.56), DHFR (OR=9.6), and CENPF (OR=6.11) were significant. Log-odds were used as weights. For the high expression(median and above) of gene as 1 and low expression as 0: 3GPS=2.4*CDCA2+ 2.3*DHFR +1.8*CENPF A cut-off of 2.4 was chosen as CDCA2 had the highest positive concordance rate (90.91%) versus DHFR (86.36%) and CENPF (77.27%). External Validation: In the CoMMpass dataset, the sensitivity and specificity for the presence of high expression of any of the 3 genes with ≥2 Proliferation Index (PI) were 92.4% and 73.8%, respectively (AUC=83.1%). The median 3GPS was 0 for <2 PI (n=238) and 6.5 for ≥2 PI (n=356). The sensitivity and specificity for the 3GPS in predicting ≥2 PI were 82.6% and 93.6%, respectively (AUC=88.1%). Pathway Analysis: Significant pathways using Reactome include polo-like kinase mediated events in G2/M transition, condensation of prometaphase chromosomes in metaphase, resolution of sister chromatid cohesion in anaphase, and APC-Cdc20 mediated degradation of Nek2A for regulation of the cell cycle. p53 signaling, cancer pathways, and microtubule regulation were also mapped. Survival Analysis: In our cohort, for CDCA2 quartiles (Q)3 and Q4, for CENPF Q3 and Q4, and for DHFR Q4 were associated with inferior overall survival. 3GPS ≥2.4 was associated with inferior survival of 60.28 months versus 111.5 months for <2.4 (p<0.01). In the validation dataset, median survival was not reached at 100 months (vs. high 79.7, p<0.01). The multivariate Cox model found 3GPS score ≥2.4 as an independent predictor (HR=1.64, 95% CI: 1.23 - 2.19), along with ECOG status, ISS stage, gender, age, and whether the patient underwent Stem Cell Transplant. Conclusion: CDCA2, DHFR, and CENPF are associated with ≥ 2% PCLI. The 3GPS score can serve as a measure of gene-based proliferation index. Prospective validation is needed for clinical practice.