Distinguishing pustular psoriasis and acute generalized exanthematous pustulosis on the basis of plasmacytoid dendritic cells and MxA protein

BACKGROUND

Distinguishing acute generalized exanthematous pustulosis (AGEP) and pustular psoriasis (PS) can be challenging. Staining for plasmacytoid dendritic cells, or PDCs (producer of IFN-α/β), and MxA (an IFN-α/β inducible protein) may help discriminate these entities.

METHODS

Forty-three cases of AGEP and PS were compiled from two academic institutions. All cases were examined for CD123+ PDCs, eosinophils, acanthosis, papillomatosis, suprapapillary plate thinning, tortuous dilated capillaries, single necrotic keratinocytes, papillary dermal edema, vasculitis, eosinophil exocytosis, intraepidermal pustules, and subcorneal pustules. A subset of cases (n = 26) was stained for MxA.

RESULTS

Perivascular and intraepidermal PDCs, dilated tortuous vessels, and MxA expression in the dermal inflammatory infiltrate were significantly (P < 0.05) in favor of a diagnosis of PS. The absence of PDCs and presence of eosinophils favored a diagnosis of AGEP (P < 0.05).

CONCLUSIONS

We found compelling evidence for the use of CD123 to highlight PDCs in these cases. The presence of PDCs and expression of MxA in dermal inflammatory infiltrate, as well as absence of eosinophils and presence of tortuous dilated capillaries favored a diagnosis of PS. Expression of MxA in the dermal infiltrate corresponds with a Th1 pathway in PS and may indicate a Th1 component in the early initial phase of AGEP.

Morphologic and Immunohistochemical Characteristics of Anorectal Melanoma

Anorectal melanoma is a rare aggressive disease. Due to its rarity and considerable histologic and immunohistochemical variabilities, misdiagnosis as lymphoma, carcinoma, sarcoma, and/or gastrointestinal stromal tumor is not uncommon, particularly in amelanotic cases. We reviewed histologic features and immunohistochemical stains of 19 anorectal melanoma cases. Histopathologic features were evaluated including junctional activity, melanin pigment, and morphologic features. Immunohistochemical stains were performed using Sox10, S100 protein, HMB-45, melan-A, CD56, and cytokeratins. Epithelioid histopathologic morphology was observed in 63.2% of the cases followed by 47.4% of the cases with spindle-cell, 26.3% with lymphoma-like, and 26.3% with pleomorphic morphologies. Junctional melanocytic activity was seen in almost half of the cases. Melanin pigment was absent (amelanotic) in nearly 40% of the cases. Immunohistochemically, diffuse positive expression of Sox10, S100 protein, melan-A, and HMB-45 was seen in 100%, 40%, 53.3%, and 38.5% of the cases, respectively. Cytokeratins were negative and CD56 was positive in 2 cases. These findings indicate that anorectal melanomas often show one or combined histolopathologic features without presence of melanin pigment and absence of junctional melanocytic activity. Anorectal melanoma should be kept in mind in the differential diagnosis of malignant neoplasms of anorectal region with epithelioid, spindle-cell, lymphoma-like, and pleomorphic morphologies. Sox10 immunohistochemistry stain can be used as a first-line screening tool to avoid extensive or unnecessary workups and/or potential misdiagnosis.

Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors

Current use of liquid biopsy is based on cell-free DNA (cfDNA) and the evaluation of mutations or methylation pattern. However, expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate cell-free total nucleic acid (cfDNA) and used targeted next generation sequencing to sequence cell-free RNA (cfRNA) and cfDNA as new approach in liquid biopsy. We demonstrate that cfRNA is overall more sensitive than cfDNA in detecting mutations. We show that cfRNA is reliable in detecting fusion genes and cfDNA is reliable in detecting chromosomal gains and losses. cfRNA levels of various solid tumor biomarkers were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers and cfRNA myeloid markers were all higher in lymphoid and myeloid neoplasms, respectively as compared with control (P < 0.0001). Using machine learning we demonstrate cfRNA was highly predictive of diagnosis (AUC >0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (P < 0.0002). This data suggests that liquid biopsy combining analysis of cfRNA with cfDNA is practical and may provide helpful information in predicting genomic abnormalities, diagnosis of neoplasms and evaluating both the tumor biology and the host response.

Bartonellosis in transplant recipients: A retrospective single center experience

BACKGROUND

Bartonellosis is a rare but challenging condition to diagnose with a spectrum of clinical presentations in the immunocompromised host.

AIM

To further characterize the presentation of Bartonella henselae (B. henselae) infections in solid organ and hematopoietic stem cell transplant recipients.

METHODS

We conducted a single-center retrospective study of all B. henselae testing for 5012 transplant recipients receiving care at a single institution between 2011 and 2018.

RESULTS

We identified 38 patients who underwent testing for B. henselae, and three of 38 were found to have bartonellosis. Two of the patients were renal transplant recipients who presented with visceral bartonellosis and symptoms concerning for post-transplant lymphoproliferative disorder. One autologous stem cell transplant recipient presented with cat scratch disease. We detail the clinical courses of these three cases and review the literature concerning the clinical presentations, differential diagnosis, and limitations of diagnostic tests for B. henselae infections in transplant recipients.

CONCLUSION

Although the incidence of B. henselae infection in transplant recipients is unknown, it merits inclusion in the differential diagnosis for fever of unknown origin in this population.

Transfusion Medicine Equations Made Internet Accessible

Multiple mathematical equations inform the practice of transfusion medicine. These equations apply to a wide range of topics: dosage of blood products, calculation of fluid volumes, and even specific treatment decisions (e.g. corrected count increment for determination of platelet refractoriness). The calculation of these equations can be complicated, prone to error, and time-consuming. A trusted source is needed to accurately perform these calculations 24 hours a day without error and without monetary cost. We sought to build internet-enabled calculators relevant to the practice of transfusion medicine. We partnered with MDCalc, an online host of medical calculators with 1 million monthly users in 196 countries, to design and host the calculators. The calculators guide users in the application of transfusion medicine equations by providing indications for use, inputs for the equations variables, error-checking, warnings for bad inputs, and interpretive guidance of the result. The following calculators were built: blood volume, corrected count increment (CCI), plasma dosage, cryoprecipitated antihemophilic factor dosage, approximate number of units for compatibility testing, maternal-fetal hemorrhage Rh(D) immune globulin dosage, intrauterine RBC transfusion dosage, neonatal polycythemia partial exchange, theoretical removal of a substance by plasmapheresis, sickle cell RBC exchange volume, peripheral blood stem cell collection, and a calculator relevant to donor lymphocyte infusion. Clinicians can now utilize this reputable and highly visible online source to access these common transfusion medicine equations at any time with an internet-enabled device (https://www.mdcalc.com/search?filter=transfusion+medicine).

Homologous Recombination Abnormalities Associated With BRCA1/2 Mutations as Predicted by Machine Learning of Targeted Next-Generation Sequencing Data

Background

Homologous recombination deficiency (HRD) is the hallmark of breast cancer gene 1/2 (BRCA1/2)-mutated tumors and the unique biomarker for predicting response to double-strand break (DSB)-inducing drugs. The demonstration of HRD in tumors with mutations in genes other than BRCA1/2 is considered the best biomarker of potential response to these DSB-inducer drugs.

Objectives

We explored the potential of developing a practical approach to predict in any tumor the presence of HRD that is similar to that seen in tumors with BRCA1/2 mutations using next-generation sequencing (NGS) along with machine learning (ML).

Design

We use copy number alteration (CNA) generated from routine-targeted NGS data along with a modified naïve Bayesian model for the prediction of the presence of HRD.

Methods

The CNA from NGS of 434 targeted genes was analyzed using CNVkit software to calculate the log2 of CNA changes. The log2 values of various sequencing reads (bins) were used in ML to train the system on predicting tumors with BRCA1/2 mutations and tumors with abnormalities similar to those detected in BRCA1/2 mutations.

Results

Using 31 breast or ovarian cancers with BRCA1/2 mutations and 84 tumors without mutations in any of 12 homologous recombination repair (HRR) genes, the ML demonstrated high sensitivity (90%, 95% confidence interval [CI] = 73%-97.5%) and specificity (98%, 95% CI = 90%-100%). Testing of 114 tumors with mutations in HRR genes other than BRCA1/2 showed 39% positivity for HRD similar to that seen in BRCA1/2. Testing 213 additional wild-type (WT) cancers showed HRD positivity similar to BRCA1/2 in 32% of cases. Correlation with proportional loss of heterozygosity (LOH) as determined using whole exome sequencing of 51 samples showed 90% (95% CI = 72%-97%) concordance. The approach was also validated in an independent set of 1312 consecutive tumor samples.

Conclusions

These data demonstrate that CNA when combined with ML can reliably predict the presence of BRCA1/2 level HRD with high specificity. Using BRCA1/2 mutant cases as gold standard, this ML can be used to predict HRD in cancers with mutations in other HRR genes as well as in WT tumors.

Coccygeal Polypoid Eccrine Nevus

Skin tags are fairly common lesions usually seen in adults on the neck and in body folds. The sacrococcygeal region is an unusual location for skin tags in children and may represent a congenital malformation of the spine or an isolated skin lesion. In this review, we summarize the clinical presentation, histopathologic changes, and differential diagnosis of coccygeal polypoid eccrine nevus as a rare cause of sacrococcygeal papules in children.

Liquid biopsy for evaluating mutations and chromosomal aberrations in cerebrospinal fluid from patients with primary or metastatic CNS tumors

Background

Cytopathology analysis of cerebrospinal fluid (CSF) is limited in detecting tumors in patients with suspected primary or metastatic central nervous system (CNS) malignancy. We investigated the use of CSF liquid biopsy (LBx) to detect neoplastic processes in the CNS.

Methods

Cell-free DNA (cfDNA) from the CSF of patients with suspected metastatic (N = 106) or primary CNS (N = 23) tumors was deep sequenced using a 302-gene panel.

Results

Four samples (3 %) (3 metastatic and 1 primary) failed sequencing quality control criteria. Metastatic tumor was confirmed in 84 (82 %) of the 103 patients suspected of metastatic tumor. Primary CNS tumor was confirmed in 11 of 22 (50 %) patients suspected of CNS tumor. Chromosomal abnormalities were detected in 55 samples (54 %). Germline mutations were detected in 23 (22 %) patients with metastatic tumors and in 1 (5 %) with a primary CNS tumor. Of the 29 patients with metastatic breast cancers, 2 (7 %) had mutations in ESR1 and 9 (31 %) had mutations in PIK3CA. Of the 21 patients with metastatic lung cancer, 9 (43 %) had EGFR mutations and 5 (24 %) had KRAS mutations. Upon comparing CSF LBx with peripheral blood LBx in 14 patients, 13 (93 %) showed only CHIP and one patient showed CNS primary tumor mutation. Serial samples from 14 patients demonstrate that CSF LBx can be used for monitoring therapy efficacy.

Conclusions

LBx using CSF is clinically reliable and provides informative results in a substantial proportion of patients with metastatic CNS tumors and to a lesser degree in patients with primary CNS tumors.

Combining cell-free RNA (cfRNA) with cell-free total nucleic acid (cfTNA) as a new paradigm for liquid biopsy

3048

Background: Expressed RNA can capture mutations, gene fusions, and biomarker profiles. In principle, each abnormal cell has one copy of mutated gene, but numerous copies of mutated RNA. Cell-free RNA (cfRNA) is not used due to the assumption that it is degraded. Next Generation Sequencing (NGS) by design is particularly adaptable for fragmented DNA and RNA. We developed an approach to isolate cell-free total nucleic acid (cfTNA) and cell-free RNA (cfRNA) from peripheral blood. Using targeted sequencing, we explored the potential of this approach to detect mutations, fusion mRNA, and copy number variation (CNV) in solid tumors and hematologic neoplasms. Methods: Peripheral blood cfTNA and cfRNA were extracted from B-cell lymphoid neoplasms (#105), T-cell neoplasms (#16), Myeloid neoplasms (#73), solid tumors (#44), and Normal individuals (#51), and sequenced using a targeted panel of 1459 genes. Results: Numbers of mutations detected in solid tumors and hematologic neoplasms were significantly (P > 0.0001) higher in cfRNA (No. = 1229) than in cfTNA (No. = 1004). Overall variant allele frequency (VAF) was significantly higher in cfRNA than in cfTNA (P < 0.0001). However, numerous mutations detected by RNA were not detected by cfTNA and vice versa. In general, nonsense mutations were more likely to be detected by cfTNA than by cfRNA and at higher VAF. Low-level mutations (VAF < 10%) were more likely to be detected by cfRNA than by cfTNA. For example, 136 mutations in TP53 gene were detected using cfRNA and only 70 mutations were detected in cfTNA. KRAS mutations were also higher in cfRNA (#33) as compared with cfTNA (#21). In contrast, when most of the mutations were nonsense, as in ASXL1 gene, more mutations were detected by cfTNA (24 vs 23). When mutations were detected in both cfRNA and cfTNA, mutation load (level of mutant copies) was overall slightly higher in cfTNA (P = 0.06), likely due to higher degradation of RNA, but varied significantly dependent on the type of mutated gene and type of mutation. cfRNA was reliable in detecting fusion transcripts in solid tumors and in hematologic neoplasms (SLC34A2-ROS1, DDX5-BCL6, ETV6-RUNX1, RUNX1T1-RUNX1, PML-RARA, RUNX1-ZFPM2, DEK-NUP214, EP300-ZNF384) irrespective of the breakpoint or partner gene. The cfTNA detected various CNVs expected by cytogenetic analysis when tumor fraction was adequate (VAF > 10%). Conclusions: This data demonstrates that using cfRNA and cfTNA provides complementary comprehensive information for evaluating mutations, fusion genes, and CNV. This approach increased sensitivity and reliability of liquid biopsy. Furthermore, the cfRNA provides critical information on relative expression of various genes that can be used as biomarkers in characterizing the neoplastic process (see ASCO abstract, Liquid Biopsy Based on Cell-Free RNA and Biomarkers profiling of hematologic and solid tumors).

Clinical and genetic characteristics in two cases of Birt-Hogg-Dubé syndrome associated with papillary renal cell carcinoma and rare Folliculin (FLCN) variants

Birt-Hogg-Dubé syndrome (BHDS) is characterized by autosomal dominant alterations in the Folliculin (FLCN) gene, resulting in cutaneous, pulmonary, and renal abnormalities. In particular, affected individuals are susceptible to the development of renal cell carcinoma (RCC), which most frequently present as chromophobe tumors or hybrid cancers with features of oncocytoma and chromophobe RCC. Type 1 and type 2 papillary neoplasms have rarely been described in the setting of BHDS, and we present two additional cases. Utilizing next-generation sequencing, the patients were found to harbor germline FLCN variants that are not well-documented in the medical literature. While RCCs associated with BHDS are thought to portend a better prognosis compared to their non-syndromic counterparts, the patients described here experienced variable clinical outcomes-one developed locally aggressive disease, distant metastases, and quickly succumbed to his disease.

Cell-free RNA in liquid biopsy and biomarkers profiling of hematologic and solid tumors

3047

Background: Expressed RNA can capture mutations, changes in expression levels due to methylation, and provide information on cell of origin, growth, and proliferation status. We developed an approach to isolate fragmented RNA from peripheral blood plasma and explored its potential to be used in liquid biopsy. Methods: Peripheral blood cfRNA was extracted from patients with neoplasms in B-cell (#105), T-cell (#16), Myeloid (#73), and from solid tumors (#44), Normal individuals (#51), and reactive post-transplant (#137). RNA was sequenced using a 1459-gene panel. Expression profile was generated using Cufflinks. Results: cfRNA levels of various solid tumor biomarkers (CA-125, CA-15-3, CEA 8, Keratin19, Keratin6A...) were significantly higher (P < 0.0001) in samples from solid tumors as compared with normal control. Similarly, cfRNA lymphoid markers (CD19, CD22, CD79A, and CD79B...) and cfRNA myeloid markers (CD33, CD14, CD117, CD56...) were all higher in B-cell lymphoid neoplasms and myeloid neoplasms, respectively (P < 0.0001), as compared with control. In evaluating the host immune system, cfRNA CD4:CD8B and CD3D:CD19 ratios in normal controls were as expected (median: 5.92 and 6.87, respectively) and were significantly lower in solid tumors (median 3.40 and 2.23, respectively, P < 0.0002). Solid tumor cfRNA showed CTLA4:CD8B ratio significantly higher in tumors than in normal (median 0.74 vs 0.19, P = 0.0001), while there was no difference in cfRNA PD-L1:CD8B ratio (median 1.45 vs 1.77, P = 0.96). Similar distinct patterns are noted for various cytokine and chemokines. cfRNA was highly predictive of diagnosis (AUC > 0.98) of solid tumors, B-cell lymphoid neoplasms, T-cell lymphoid neoplasms, and myeloid neoplasms as compared with normal control. When a specific neoplastic disease was considered against all cases including control and other neoplasms, the AUC varied between 0.77 and 0.949. Conclusions: This data shows that liquid biopsy using targeted sequencing of cfRNA in patients with various types of cancer provides comprehensive and reliable information on the neoplastic disease as well as the host. [Table: see text]

Concordance Between the TIRADS Ultrasound Scoring Criteria, Fine-Needle Aspiration Cytology, and Thyroid Final Resection Diagnosis

Objectives

Thyroid imaging reporting and data system (TIRADS) criteria were recently introduced in our institution to aid in predicting diagnosis for various thyroid lesions. We evaluated the association of TIRADS imaging score and fine-needle aspiration (FNA) cytology with thyroid lesions that had a confirmed diagnosis at resection, with a focus on understanding the predictability of this diagnostic tool in malignancy prediction.

Methods

We assessed the concordance of TIRADS criteria and FNA diagnosis to the final anatomical diagnosis in the assessment of thyroid lesions. We retrieved the cases from the archives of the Yale pathology department between June 2017 and January 2018. Our inclusion criteria included patients who had a TIRADS score, cytology diagnosis, and final surgical resection diagnosis. A total of 65 subjects with an age range of 11 to 88 years were identified.

Results

The majority of the patients were females, 65% (42/65). Cases with TIRADS score 1-2 (likely benign) and Bethesda I/II nondiagnostic/benign were few since most of these cases did not go for surgical resection. The mildly suspicious TIRAD score 3 and FLUS category showed similar trends, 68% and 67%, respectively, in predicting malignant lesions. The TIRADS score 4 when compared to cytology (IV)/(V) demonstrated similar consistent results in malignancy prediction, both being high at 89% and 87%, respectively. The TIRADS score 5 demonstrated a 95% malignancy prediction. The overall sensitivity and specificity of TIRADS score in our cohort were 66% and 77%, respectively. The positive and negative predictive values of TIRADS score in our cohort were 89% and 39%, respectively. In comparison, the overall sensitivity and specificity of cytology assessment in our cohort were 91% and 44%, respectively. The positive and negative predictive values of cytology assessment in our cohort were 85% and 57%, respectively.

Conclusion

Our results demonstrated that both cytology and TIRAD score had similar trends in malignancy prediction. Cytological assessment had higher sensitivity but lower specificity compared to TIRADS score. While both techniques showed concordant high predictability of malignant lesions (approximately 91%), the use of both modalities adjunctively will be very useful in triaging cases for surgery. Overall, utilizing TIRADS score with cytology will help reduce the risk of unnecessary invasive procedures in patients with a low probability of malignant thyroid disease.

Differential diagnosis of hematologic and solid tumors using targeted transcriptome and artificial intelligence

3018

Background: Diagnosis and classification of tumors is becoming increasingly dependent on biological and molecular biomarkers. RNA expression profiling using next generation sequencing (NGS) provides information on various biological and molecular changes in the cancer and in the microenvironment. We explored the potential of using targeted transcriptome and artificial intelligence (AI) in the differential diagnosis and classification of various hematologic and solid tumors. Methods: RNA from hematologic neoplasms (N = 2606) and solid tumors (N = 2038) as well as normal bone marrow and lymph node control (N = 806) were sequenced by NGS using a targeted 1408-gene panel. The hematologic neoplasms included 20 different subtypes. Solid tumors included 24 different subtypes. Machine learning is used for comparing two classes at a time. Geometric Mean Naïve Bayesian (GMNB) classifier is used to provide differential diagnosis across 45 diagnostic entities with assigned ranking. Results: Machine learning showed high accuracy in distinguishing between two diagnoses with AUC varied between 1 (Sarcoma vs GIST) and 0.841 (MDS vs normal control) (examples in Table). For differential diagnosis between all 45 different diagnoses, we used 3045 samples for training the GMNB algorithm and 1415 samples for testing. Correct first choice diagnosis was obtained in 100% of ALL, 88% of AML, 85% of DLBCL, 82% of colorectal cancer, 88% of lung cancer, 72% of CLL, and 72% of follicular lymphoma. The algorithm had difficulty in typically overlapping diagnoses and diagnosed as first choice 19% of MDS, 46% of normal, and 12% of MPN. Diagnosis improved significantly when second choice was considered. Conclusions: Targeted RNA profiling with proper AI can provide highly useful tools for the pathologic diagnosis and classification of various cancers. Additional information such as mutation profile and clinical information can improve these algorithms, reduce subjectivity, and minimize errors in pathologic diagnoses. [Table: see text]

Expanding the clinical utility of liquid biopsy by using liquid transcriptome and artificial intelligence

Most of the current utilization of liquid biopsy (LBx) is based on analyzing cell-free DNA(cfDNA). There is limited data on using cell-free RNA (cfRNA) levels (liquid transcriptome) in LBx. The major hurdles for using liquid transcriptome is its low level in circulation and the dilutional effects of various tissues that may pour their RNA into circulation. We explored the potential of using artificial intelligence (AI) to normalize the cancer-specific cfRNA and to enable liquid transcriptome to predict diagnosis. cfRNA transcriptomic data from 1009 peripheral blood samples was generated by hybrid capture next generation sequencing (NGS). Using two-thirds of samples for training and one third for testing, we demonstrate that AI is able to distinguish between normal control (N = 368) and patients with solid tumors (N = 404) with AUC = 0.820 (95 % CI: 0.760-0.879), patients with myeloid neoplasms (N = 99) with AUC = 0.858 (95 % CI: 0.793-0.924) and patients with lymphoid neoplasms (N = 128) with AUC = 0.788 (95 % CI: 0.687-0.888). Specific diagnosis was also possible when patients with lung, breast, colorectal, and myelodysplastic subgroups were tested. This data suggests that liquid transcriptomics when used with AI has the potential of transforming "liquid biopsy" to "true" biopsy, replacing the need for tissue biopsy.

Intravascular Large B-Cell Lymphoma: Clinical and Histopathologic Findings

Intravascular large B-cell lymphoma (IVLBCL) is a rare subset of extranodal non-Hodgkin lymphoma characterized by neoplastic lymphocytes within the lumina of small to medium-sized blood vessels. IVLBCLs are B-cell tumors that can present in essentially any organ system, including the skin. Cutaneous manifestations vary greatly and can mimic other skin disease which may delay diagnosis; in the absence of skin lesions, blind skin biopsies can be utilized for diagnosis. Early studies suggested that IVLBCL is a very aggressive lymphoma with high overall mortality rate and short survival times. However, earlier diagnosis and use of new treatment modalities have shown promise in recent studies. This case series illustrates the heterogeneity of clinical and pathologic presentations of this uncommon lymphoma.