Pathogenicity Prediction of Gene Fusion in Structural Variations: A Knowledge Graph-Infused Explainable Artificial Intelligence (XAI) Framework.

When analyzing cancer sample genomes in clinical practice, many structural variants (SVs), other than single nucleotide variants (SNVs), have been identified. To identify driver variants, the leading candidates must be narrowed down. When fusion genes are involved, selection is particularly difficult, and highly accurate predictions from AI is important. Furthermore, we also wanted to determine how the prediction can make more reliable diagnoses. Here, we developed an explainable AI (XAI) suitable for SVs with gene fusions, based on the XAI technology we previously developed for the prediction of SNV pathogenicity. To cope with gene fusion variants, we added new data to the previous knowledge graph for SVs and we improved the algorithm. Its prediction accuracy was as high as that of existing tools. Moreover, our XAI could explain the reasons for these predictions. We used some variant examples to demonstrate that the reasons are plausible in terms of pathogenic basic mechanisms. These results can be seen as a hopeful step toward the future of genomic medicine, where efficient and correct decisions can be made with the support of AI.

A longitudinal analysis of paroxysmal nocturnal haemoglobinuria-type cells in patients with bone marrow failure: Results of a prospective multi-centre study in Japan.

To determine the prevalence and clinical relevance of glycosylphosphatidylinositol-anchored protein-deficient (GPI[-]) cell populations (paroxysmal nocturnal haemoglobinuria [PNH]-type cells) in patients with acquired aplastic anaemia (AA) or myelodysplastic syndrome (MDS), we prospectively studied peripheral blood samples of 2402 patients (1075 with AA, 900 with MDS, 144 with PNH, and 283 with other anaemia) using a high-sensitivity flow cytometry assay in a nationwide multi-centre observational study. PNH-type cells were detected in 52.6% of AA and 13.7% of MDS patients. None of the 35 patients with refractory anaemia (RA) with ringed sideroblasts or the 86 patients with RA with excess of blasts carried PNH-type cells. Among the 317 patients possessing PNH-type granulocytes, the percentage of PNH-type granulocytes increased by ≥10% in 47 patients (14.8%), remained unchanged in 240 patients (75.7%), and decreased by ≥10% in 30 patients (9.5%) during 3 years of follow-up. PNH-type granulocyte expansion occurred more frequently (27.1%) in the 144 patients who originally carried PNH-type granulocytes ≥1% than in the 173 patients with PNH-type granulocytes <1% (4.6%). This study confirmed that PNH-type cells are undetectable in authentic clonal MDS patients, and the presence of ≥1% PNH-type granulocytes predicts a higher likelihood of PNH-type cell expansion than with <1% PNH-type granulocytes.

Mitigating Drug-Target-Drug Complexes in Patients With Paroxysmal Nocturnal Hemoglobinuria Who Switch C5 Inhibitors.

Drug-target-drug complexes (DTDCs) are phenomena newly observed in patients who switch from the complement component 5 (C5) inhibitor eculizumab to crovalimab, a novel, anti-C5 antibody in development for paroxysmal nocturnal hemoglobinuria (PNH), because these agents bind to different C5 epitopes. In Part 3 of the four-part, phase I/II COMPOSER study, 19 patients with PNH switching from eculizumab received 1,000-mg crovalimab intravenously, then subcutaneous maintenance doses from Day 8 (680 mg every 4 weeks (q4w), 340 mg every 2 weeks, or 170 mg every week). Crovalimab exposure was transiently reduced, and size-exclusion chromatography and crovalimab-specific enzyme-linked immunosorbent assays revealed DTDCs in all 19 patients' sera. Additionally, self-limiting mild to moderate symptoms suggestive of type III hypersensitivity reactions occurred in two patients. Mathematical modeling simulations of DTDC kinetics and effects of dosing on DTDC size distribution using Part 3 data predicted that increased crovalimab concentrations could reduce the proportion of large, slow-clearing DTDCs in the blood. A simulation-guided, optimized crovalimab regimen (1,000 mg intravenously; four weekly, subcutaneous 340-mg doses; then 680 mg q4w from Day 29) was evaluated in Part 4. Confirming the model's predictions, mean proportions of large DTDCs in patients who switched from eculizumab to this optimized regimen decreased by > 50% by Day 22, and target crovalimab concentrations were maintained. No type III hypersensitivity reactions occurred in Part 4. Optimizing crovalimab dosing thus reduced the proportion of large DTDCs, ensured adequate complement inhibition, and may improve safety. Model-based dosing optimization to mitigate DTDC formation offers a useful strategy for patients switching to novel antibody treatments targeting soluble epitopes.

Donor stem cell-derived paroxysmal nocturnal hemoglobinuria after umbilical cord blood transplantation.

Donor cell-derived hematological disorder (DCHD) is a rare complication of allogeneic hematopoietic stem cell transplantation (HSCT). The number of reports of DCHD has been increasing in the last decade, which likely reflects the growing number of HSCTs and the improved ability to identify the donor cell origin. Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired hematological disorder arising in the context of clonal expansion of hematopoietic stem cells harboring a somatic mutation in phosphatidylinositol glycan anchor biosynthesis, class A. We report here a patient with adult T-cell leukemia/lymphoma, who developed PNH 7 years after umbilical cord blood transplantation. The patient has maintained complete remission with full-donor chimerism after HSCT. Thus, PNH was derived from stem cells of donor origin. The immature immune environment in the recipient after cord blood transplantation might have contributed to the rapid clonal expansion for neonatal stem cells in cord blood to develop typical symptomatic PNH in a short period. To the best of our knowledge, this is the first report in the literature of a case of PNH that developed in donor stem cells after HSCT.

Dramatic response of chemotherapy for cancer of unknown primary origin of sarcomatoid carcinoma producing granulocyte colony-stimulating factor.

Cancer of unknown primary origin (CUP) which is usually diagnosed based on the histological type of metastatic site has marked heterogeneous characteristics. Sarcomatoid carcinoma defined as CUP has not been reported according to our literature survey. A 59-year-old man presented with enlarged multiple thoracic lymph nodes, huge splenomegaly and nodules in left temporal lobe of the brain. The histopathological diagnosis of lymph node and spleen was sarcomatoid carcinoma. However, all extensive diagnostic examinations could not detect a site of primary origin. The laboratory data showed marked leukocytosis with increased serum granulocyte colony-stimulating factor (G-CSF). Therefore, the patient was finally diagnosed of CUP of sarcomatoid carcinoma producing G-CSF. After gamma knife treatment for brain metastases, two regimens of taxan-based chemotherapy (carboplatin and paclitaxel, gemcitabine and docetaxel) were administered, with no effect but further tumor progression. Splenectomy for avoiding splenic rupture was performed. As the third line chemotherapy, the combination consisting of doxorubicin and ifosfamide was administered and showed a good therapeutic effect and normalized white blood cell count and serum G-CSF level. He achieved complete remission after three cycles. Herein we present an extremely rare case of CUP of sarcomatoid carcinoma producing G-CSF. Our case suggests the importance of chemotherapy including doxorubicin and ifosfamide, and multimodal therapeutic strategy for this aggressive disease.

Synchronous primary lung cancer presenting with small cell carcinoma and adenocarcinoma.

Multiple synchronous primary lung cancers presenting with different histologic types are uncommon. Among reported cases with different histologic findings, only a few had small cell lung cancer (SCLC) and adenocarcinoma. This unusual combination of lung cancers has not been well reported. In this report, we describe two cases of synchronous primary lung cancer presenting with lymph node metastasis of SCLC and early-stage adenocarcinoma. Epidermal growth factor receptor (EGFR) mutation was not detected in either SCLC or adenocarcinoma in the two cases.

[Development of chronic myelogenous leukemia during treatment with TPO receptor agonist for ITP].

We report a 77-year-old Japanese man with idiopathic thrombocytopenic purpura (ITP) which developed into chronic myelogenous leukemia (CML) during treatment with eltrombopag, a thrombopoetin (TPO) receptor agonist, because the disease was refractory to prednisolone. Eltrombopag can induce a good reaction in terms of the platelet count. However, CML in the chronic phase developed in about 19 months in our present case. Dasatinib was administered because he had diabetes. However, a blastic crisis immediately occurred. He died despite switching to Nilotinib. Recently, the occurrence of myelofibrosis and hematological malignancies due to long-term use of TPO receptor agonists has become a concern. This is the first report of a TPO receptor agonist possibly contributing to CML onset and crisis.

[Definitive diagnosis of intravascular large B-cell lymphoma by random skin biopsy].

A 69-year-old male was admitted to our hospital for high-grade-fever and body weight loss lasting for a few months. In a previous hospital, extensive laboratory examinations and imaging modalities had failed to establish the origin of the fever. On admission he showed mild anemia, and elevated LDH and CRP, together with a high sIL-2R level, suggesting a possibility of lymphoid malignancy without nodal or solid organ involvements, in particular, intravascular large B-cell lymphoma(IVLBCL). A bone marrow biopsy revealed no abnormal findings except minimal hemophagocytosis. A random skin biopsy was then performed, though no detectable skin lesion was seen. The histological results of the skin materials clearly showed a prominent intravascular large lymphoid cell proliferation with a phenotype of CD20+, CD79a+, CD3- and CD5- in the small vessels. On the basis of these findings, a diagnosis of IVLBCL was established and the patient was treated with(R-)CHOP regimen immediately, which resulted in complete remission following two courses of chemotherapy. Difficulties often arise in the diagnosis of IVLBCL when suspicious lesions suitable for biopsy are lacking. Random skin biopsy would therefore be a useful tool if less invasive measures fail.