Citations

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.

Severe COVID-19 is a multisystem condition with thromboinflammation as a significant driver of morbidity and mortality. Cellular components involved in inflammatory and coagulation responses include platelets, endothelium, monocytes, and neutrophils. Thrombotic manifestations, such as arterial thrombosis, venous thromboembolism, and tissue microthrombosis, occur in at least 20% of ICU COVID-19 patients, possibly more based on postmortem studies. This study investigates the presence of prothrombotic antibodies similar to those found in heparin-induced thrombocytopenia (HIT), a condition caused by platelet-activating antibodies targeting platelet factor 4 (PF4) when complexed with heparin (PF4/H). In a study of samples from 130 hospitalized patients collected on average 3.6 days after COVID-19 diagnosis, 80% were found to have IgG antibodies recognizing PF4/H. This percentage is significantly lower than in 22 HIT patients (100%) but higher than in 51 non-COVID-19 patients with acute respiratory symptoms (ARS) (25%) and 12 healthy subjects (0%). Additionally, 41% of the 130 patients had antibodies inducing PF4-dependent P-selectin expression in CpG-treated normal platelets, a rate significantly lower than in 12 HIT patients (100%) but higher than in 51 non-COVID-19 ARS patients (20%) and 12 healthy subjects (0%). Significantly, platelet-activating antibodies in COVID-19 patients were associated with a specific elevation of platelet α-granule proteins in the plasma and correlated with inflammation and tissue damage markers, suggesting these antibodies' functionality in patients. Significantly, unlike HIT, both PF4/H-reactive and platelet-activating antibodies were found in COVID-19 patients regardless of recent heparin exposure, indicating different antigenic stimuli for these antibodies in COVID-19. Notably, certain antibodies against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 possessed sequence motifs, RKH and Y5, in the heavy-chain complementarity-determining region 3 (HCDR3) resembling those in pathogenic HIT antibodies identified in our previous studies, suggesting that these antibodies can activate platelets. Introducing exogenous RBD to COVID-19 plasma or IgG purified from COVID-19 plasma significantly reduced their ability to activate platelets. Furthermore, immunodepleting RBD-reactive antibodies from COVID-19 plasma or IgG purified from COVID-19 plasma using RBD-coated beads significantly reduced their ability to activate platelets. These findings demonstrate that some RBD-specific plasma IgG antibodies can activate platelets. To demonstrate the presence of RBD-specific, platelet-activating antibodies at the clonal level, we produced recombinant antibodies from 42 RBD-binding IgG+ B cells, tested their ability to activate platelets, and identified four that could do so. Interestingly, three antibodies possess HCDR3 sequences resembling RKH or Y5 motifs. Additionally, we identified RKH or Y5 motifs in RBD-specific antibodies reported by other groups, produced 15 such antibodies recombinantly, tested their ability to activate platelets, and identified four more that could do so. IgG+ B cells with these HCDR3 motifs were markedly expanded in severe COVID-19 patients, suggesting an expansion of B cells producing platelet-activating antibodies. The demonstration of functional and structural similarities between certain RBD-specific antibodies in COVID-19 patients and pathogenic HIT antibodies suggests a novel mechanism by which RBD-specific antibodies might contribute to thrombosis in COVID-19.

Multiple myeloma (MM) is an incurable plasma cell (PC) malignancy. Despite therapeutic advances that have vastly improved survival, all patients are expected to relapse. Current standard of care includes autologous stem cell transplant (ASCT) with high-dose melphalan (HDM) administered as a conditioning agent. Cytotoxic chemotherapies such as melphalan have been shown to drive therapy-induced senescence (TIS) in several tissues. We hypothesize that HDM activates TIS pathways in surviving MM cells and that this may correlate with patient outcomes post-ASCT. We developed an in vitro HDM model using 5TGM1 mouse MM cells treated with vehicle (Veh) or HDM (10µM, IC90) for 6h, followed by co-culture with primary mouse bone marrow stromal cells. Image analysis was performed to quantify proliferation by cumulative population doublings (CPDs) over 10 days, after which 5TGM1 cells were evaluated for cell size, telomere-associated DNA damage foci (TAFs), sensitivity to senolysis, and senescence gene expression (scRNA-seq and RT-qPCR). The effect of HDM on CPDs and cell size was also evaluated in human MM cell lines RPMI-8226 and H929. scRNA-seq was used to analyze CD138+ PCs from MM patients at various timepoints post-ASCT. Longitudinal MM patient iliac crest biopsies (diagnosis, post-ASCT; N=20) were stained for CD138+ PCs; PC burden was quantified by AI-assisted histology. Lastly, we established an in vivo model of induction therapy (bortezomib) followed by HDM/SCT in Vk*MYC mouse MM engrafted C57BL/6 mice. Tumor burden was tracked by serum protein electrophoresis for M-spike using submandibular bleeds. Bone marrow was then flushed from long bones and analyzed by flow cytometry and immunofluorescence. HDM-5TGM1 showed decreased CPDs (HDM 0.32±0.31, Veh 6.72±0.69, p<0.0001, N=3), increased size (median pixel size: HDM 413.2±99.98, Veh 207±8.88, p<0.05, N=3), and increased TAF+ cells (Percent TAF+ cells: HDM 34.77%±10.74%, Veh 11.41%±1.58%, p<0.05, N=3) consistent with known TIS features. Preliminary assessment (N=1) of human MM cell lines showed similar growth arrest (RPMI-8226 CPDs: HDM 0.058±0.101, Veh 4.185±0.358; H929 CPDs: HDM 0±0, Veh 4.61±0.243) and size increase (RPMI-8226 mean pixel size: HDM 804.1±6.048, Veh 526.9±2.115; H929 mean pixel size: HDM 371.2±26.95, Veh 130.3±41.43), suggesting a translatable mechanism. HDM-5TGM1 cells were more sensitive to senolysis by dasatinib+quercetin (viability: HDM 54.9%±0.09%, Veh 76.0%±0.05%, N=2). scRNA-seq analysis showed that HDM-5TGM1 were enriched for gene sets related to senescence pathways, including the published set SenMayo (FDR<0.25). HDM-5TGM1 cells also exhibited myeloid gene expression consistent with previous publications on MM dormancy. RT-qPCR confirmed significant increases in HDM-5TGM1 (p<0.001, N=3) in senescence markers (Cdkn1a, Cdkn1c, Glb1), senescent cell anti-apoptosis pathway genes (SCAPs, Bcl2l1), senescence associated secretory phenotype (SASP) genes (Ccl5, Icam1, Mmp13), and myeloid markers (Axl, Fcer1g, Mpeg1). scRNA-seq of patient CD138+ PCs confirmed a myeloid-like cluster that gained prominence in relapsed patients with resistant disease. CD138+ PCs were detected in patient bone biopsies post-ASCT. Interestingly, patients who relapsed (≤3 years, N=9) had a greater percent reduction in PC burden from diagnosis to post-ASCT when compared to patients that did not relapse (N=11) in that time (p=0.02). Further, CD138+ PC burden post-ASCT positively correlated with time in remission in relapsed patients (R=0.697, p=0.03). Bortezomib reduced serum M-spike in Vk*MYC-engrafted mice (p=0.0003); M-spike was further reduced by HDM/SCT compared to Veh-treated mice (p=0.0007). Flow cytometry confirmed a decrease in Vk*MYC cells after HDM/SCT (p=0.0043), and the percentage of Vk*MYC cells with greater size and complexity was increased compared to Veh-treated mice (p=0.0043), consistent with our in vitro data. Vk*MYC cells from HDM-treated mice also trended for more TAF+ cells (>3 TAFs) compared to Veh-treated mice (p=0.0714). Our findings suggest that HDM can induce a TIS and myeloid signature in surviving MM cells. Greater MM burden post-ASCT appears to be associated with longer durable response, again suggesting that these cells may be in growth arrest consistent with TIS. Finally, senolytics may be a novel approach to eliminate surviving MM cells and prevent relapse.

Abstract Objectives Protein-truncating variants in the TTN gene are a well-established cause of dilated cardiomyopathy (DCM). We report a novel case of DCM caused by a mobile element insertion (MEI) in TTN, through which we highlight the key features of MEIs in next-generation sequencing data. Because of the rarity of MEIs, the next-generation sequencing data features associated with these events may be mistaken as noise, potentially leading to missed diagnoses. Methods Next-generation sequencing gene panel testing for DCM was performed on a 17-year-old male patient presenting with severe left ventricular dilatation and systolic dysfunction. Manta was used for structural variant detection, followed by manual review of NGS data for potential structural variants. Results Manta detected a potential insertion in TTN. Manual review identified hallmark features consistent with a LINE-1 MEI. This finding was orthogonally confirmed by long-range polymerase chain reaction and gel electrophoresis, which indicated an insertion of approximately 4 to 5 kilobase pairs. The insertion disrupted the reading frame of TTN within an A-band exon, resulting in protein truncation that was classified as likely pathogenic. Conclusions This case expands the mutational spectrum of TTN protein-truncating variants. It also underscores the importance of recognizing rarer types of pathogenic variants (eg, MEIs) to produce accurate genetic diagnostics.

Abstract Thromboembolic complication is common in severe coronavirus disease 2019 (COVID-19), leading to an investigation into the presence of prothrombotic antibodies akin to those found in heparin-induced thrombocytopenia (HIT). In a study of samples from 130 hospitalized patients, collected 3.6 days after COVID-19 diagnosis, 80% had immunoglobulin G (IgG) antibodies recognizing complexes of heparin and platelet factor 4 (PF4; PF4/H), and 41% had antibodies inducing PF4-dependent P-selectin expression in CpG oligodeoxynucleotide–treated normal platelets. Unlike HIT, both PF4/H-reactive and platelet-activating antibodies were found in patients with COVID-19 regardless of recent heparin exposure. Notably, PF4/H-reactive IgG antibodies correlated with those targeting the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 spike protein. Moreover, introducing exogenous RBD to or removing RBD-reactive IgG from COVID-19 plasma or IgG purified from COVID-19 plasma significantly reduced their ability to activate platelets. RBD-specific antibodies capable of platelet activation were cloned from peripheral blood B cells of patients with COVID-19. These antibodies possessed sequence motifs in the heavy-chain complementarity-determining region 3 (HCDR3), resembling those identified in pathogenic HIT antibodies. Furthermore, IgG+ B cells having these HCDR3 signatures were markedly expanded in patients with severe COVID-19. Importantly, platelet-activating antibodies present in patients with COVID-19 were associated with a specific elevation of platelet α-granule proteins in the plasma and showed a positive correlation with markers for inflammation and tissue damage, suggesting a functionality of these antibodies in patients. The demonstration of functional and structural similarities between certain RBD-specific antibodies in patients with COVID-19 and pathogenic antibodies typical of HIT suggests a novel mechanism by which RBD-specific antibodies might contribute to thrombosis in COVID-19.

Background To evaluate the benefit-risk assessment of atogepant and calcitonin gene–related peptide (CGRP) monoclonal antibodies (mAbs) vs. placebo based on the number needed to treat (NNT) and the number needed to harm (NNH) in a blended episodic migraine and chronic migraine (EM + CM) population. Methods The NNT was calculated based on achievement of a ≥ 50% reduction in mean monthly migraine days (MMDs) from baseline across 12 weeks. The NNH was calculated using the proportion of participants reporting a discontinuation due to adverse events (AEs). The primary analysis included data from studies of atogepant, erenumab, galcanezumab, eptinezumab and fremanezumab. Results In the primary analysis, the calculated NNT for atogepant 60 mg vs. placebo was 4.2 (95% credible interval (CrI) = 3.1–6.7), which was the lowest relative to the CGRP mAbs in the blended EM + CM population. Participants who received atogepant 60 mg or fremanezumab showed the most favorable NNH values (−1010 (95% Crl = 44 to ∞ to number needed to benefit 80) for atogepant) resulting from lower rates of discontinuation due to AEs compared with those receiving placebo. Conclusions Atogepant demonstrated a favorable benefit-risk profile, with NNT and NNH values comparable (not statistically significant) with those of CGRP mAbs across all analyses.

Abstract Purpose: Squamous cell carcinoma of the anus (SCCA) is primarily driven by human papillomavirus (HPV) infection. Up to 30% of patients experience recurrence, necessitating improved surveillance strategies. Liquid biopsies have shown promise as a tool in oncology. This study investigates the clinical performance of circulating tumor tissue modified viral (TTMV)- HPV DNA in the post-treatment surveillance of SCCA. Patients and methods: This central IRB-approved retrospective cohort study included 117 patients diagnosed with HPV-driven SCCA from seven U.S. centers who had ≥1 TTMV-HPV DNA tests (NavDx®, Naveris, Inc., Waltham, MA) performed between March 2020 and June 2024. TTMV-HPV DNA for HPV subtypes 16, 18, 31, 33, and 35 were analyzed using droplet digital PCR. The diagnostic accuracy of TTMV-HPV DNA was evaluated by comparing test results with clinical evidence of SCCA recurrence determined through anoscopy, radiology, and/or tissue biopsy. Recurrence is defined as either a positive biopsy or subsequent salvage therapy. Results: Patients were primarily female (73%) with a median age 63 years. Median follow-up after initial treatment was 19 months. Forty-seven patients (40%) had pretreatment TTMV-HPV DNA testing, with a baseline detectability of 85.1% (40/47, 95% CI: 74.9–95.3). Of these, 24 were re-tested within 3 months post-treatment and 18 had undetectable TTMV-HPV DNA (75%). Those patients whose scores became undetectable had significantly longer recurrence-free survival than those whose scores remained detectable (log-rank test, p=0.01). One hundred and four patients (89%) underwent post-treatment testing, of which 91 provided relevant data for the analysis. Of these 91 patients, 27 (29.7%) experienced recurrence. Post-treatment testing demonstrated a per- patient sensitivity of 85.7% (24/28, 95% CI: 72.8-98.7). Of four patients with a false negative test, only one had biopsy-confirmed recurrence, whereas the remaining recurrences were not biopsied prior to starting salvage treatment. The positive predictive value of a single positive test was 97.6% (40/41; 95% CI: 92.8–100.0). One patient remains in active follow-up. Of the true positive post-treatment tests, 58% (14/24) predicted recurrence before clinical detection, with a median lead time of 59 days (range: 10–536). There were 141 negative post-treatment tests across 66 patients. This yielded a per-test specificity and negative predictive value of 99.3% (136/137, 95% CI: 97.8-100.0) and 97.2% (136/140, 95% CI: 94.9-99.9), respectively. Indeterminate TTMV-HPV DNA tests were rare (5/268,1.9%). However, clinically indeterminate findings (CIFs) were common, with 141 post-treatment CIFs identified across 52/117 patients (44.4%). TTMV-HPV DNA testing was able to correctly predict recurrence status in 94.3% of CIF cases. Conclusion: TTMV-HPV DNA testing is a sensitive and specific surveillance method for detecting early recurrence of HPV-driven SCCA. Citation Format: Shane Lloyd, Rafi Kabarriti, James Jabalee, Tyler Slater, Corbin Jacobs, Sean Inocencio, Michael Rutenberg, Chance Matthiesen, Kasha Neff, Gene-Fu F Liu, Tiffany M Juarez, Catherine DV Fitz, Stanley Liauw. Plasma-based circulating tumor tissue modified viral (TTMV)-HPV DNA for detection of recurrent HPV-driven anal cancer [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr B018.

Abstract Targeted gene expression profiling improves risk stratification for meningiomas, but the utility of this approach for low grade meningiomas is incompletely understood. To address this, 466 meningiomas that were initially used to validate a 34-gene expression biomarker were combined with 270 previously unpublished samples for an analysis of biomarker performance in newly diagnosed (n=691) or recurrent (n=45) WHO grade 1 meningiomas treated with gross total (GTR) or subtotal resection (STR), and newly diagnosed WHO grade 2 meningiomas treated with GTR. Prediction of local freedom from recurrence (LFFR) or overall survival (OS) was measured using Cox proportional hazards models and the Kaplan-Meier method. The cohort included 736 patients, 69.4% female, with a median age at diagnosis of 58 years. There were 635 WHO grade 1 meningiomas, 498 with GTR and 133 with STR, and 101 WHO grade 2 meningiomas with GTR. The median follow-up was 4.6 years, the local recurrence rate was 12.0% and the rate of death was 8.4%. The biomarker classified 51.5% of meningiomas as intermediate risk and 9.6% as high risk. Combining the biomarker with extent of resection identified 19.7% as unfavorable (intermediate molecular risk with STR or high molecular risk), including 7.4% of newly diagnosed WHO grade 1 meningiomas with GTR. The risk score was prognostic for LFFR overall (hazard ratio per 0.1 increase in risk score 1.89, 95% confidence interval 1.58-2.25) and across WHO grades, extents of resection, and newly diagnosed or recurrent settings. Gene expression risk groups were prognostic for LFFR, with improved outcomes among low molecular risk compared to intermediate molecular risk (Log-rank, p=0.0002) and high molecular risk meningiomas (Log-rank, p<0.0001). These data suggest that a targeted gene expression biomarker can identify low grade meningiomas that are more likely to recur after surgery, possibly changing management for approximately one-fifth of cases.

ABSTRACT Medically important pathogenic fungi invade vertebrate tissue and are considered primary when part of their nature life cycle is associated with an animal host and are usually able to infect immunocompetent hosts. Opportunistic fungal pathogens complete their life cycle in environmental habitats or occur as commensals within or on the vertebrate body, but under certain conditions can thrive upon infecting humans. The extent of host damage in opportunistic infections largely depends on the portal and modality of entry as well as on the host’s immune and metabolic status. Diseases caused by primary pathogens and common opportunists, causing the top approximately 80% of fungal diseases [D. W. Denning, Lancet Infect Dis, 24:e428–e438, 2024, https://doi.org/10.1016/S1473-3099(23)00692-8 ], tend to follow a predictive pattern, while those by occasional opportunists are more variable. For this reason, it is recommended that diseases caused by primary pathogens and the common opportunists are named after the etiologic agent, for example, histoplasmosis and aspergillosis, while this should not be done for occasional opportunists that should be named as [causative fungus] [clinical syndrome], for example, Alternaria alternata cutaneous infection. The addition of a descriptor that identifies the location or clinical type of infection is required, as the general name alone may cover widely different clinical syndromes, for example, “rhinocerebral mucormycosis.” A list of major recommended human and animal disease entities (nomenclature) is provided in alignment with their causative agents. Fungal disease names may encompass several genera of etiologic agents, consequently being less susceptible to taxonomic changes of the causative species, for example, mucormycosis covers numerous mucormycetous molds.